Method for producing proteins in pichia pastoris that lack detectable cross binding activity to antibodies against host cell antigens

ABSTRACT

Methods for producing proteins and glycoproteins in  Pichia pastoris  that lack detectable cross binding activity to antibodies made against host cell antigens are described. In particular, methods are described wherein recombinant  Pichia pastoris  strains that do not display a β-mannosyltransferase 2 activity with respect to an N-glycan or O-glycan and do not display at least one activity selected from a β-mannosyltransferase 1, 3, and 4 activity to produce recombinant proteins and glycoproteins. These recombinant  Pichia pastoris  strains can produce proteins and glycoproteins that lack detectable α-mannosidase resistant β-mannose residues thereon and thus, lack cross binding activity to antibodies against host cell antigens. Further described are methods for producing bi-sialylated human erythropoietin in  Pichia pastoris  that lack detectable cross binding activity to antibodies against host cell antigens.

This is a continuation of U.S. patent application Ser. No. 13/501,350, filed May 31, 2012; which is the national phase of international application no. PCT/US10/52140, filed Oct. 11, 2010; which claims the benefit of U.S. provisional patent application No. 61/252,312, filed Oct. 16, 2009; each of which are herein incorporated by reference in their entireties.

BACKGROUND OF THE INVENTION

(1) Field of the Invention

The present invention relates to methods for producing protein and glycoproteins in Pichia pastoris that lack detectable cross binding activity to antibodies made against host cell antigens. In particular, the present invention relates to using recombinant Pichia pastoris strains that do not display a β-mannosyltransferase 2 activity with respect to an N-glycan or O-glycan and do not display at least one activity selected from the group consisting of β-mannosyltransferase 1, 3, and 4 activity with respect to an N-glycan or O-glycan. These recombinant Pichia pastoris strains can produce proteins and glycoproteins that lack detectable α-mannosidase resistant β-mannose residues thereon. The present invention further relates to methods for producing bi-sialylated human erythropoietin in Pichia pastoris that lack detectable cross binding activity to antibodies against host cell antigens.

(2) Description of Related Art

The ability to produce recombinant human proteins has led to major advances in human health care and remains an active area of drug discovery. Many therapeutic proteins require the posttranslational addition of glycans to specific asparagine residues (N-glycosylation) of the protein to ensure proper structure-function activity and subsequent stability in human serum. For therapeutic use in humans, glycoproteins require human-like N-glycosylation. Mammalian cell lines (e.g., CHO cells, human retinal cells) that can mimic human-like glycoprotein processing have several drawbacks including low protein titers, long fermentation times, heterogeneous products, and continued viral containment. It is therefore desirable to use an expression system that not only produces high protein titers with short fermentation times, but can also produce human-like glycoproteins.

Fungal hosts such as the methylotrophic yeast Pichia pastoris have distinct advantages for therapeutic protein expression, for example, they do not secrete high amounts of endogenous proteins, strong inducible promoters for producing heterologous proteins are available, they can be grown in defined chemical media and without the use of animal sera, and they can produce high titers of recombinant proteins (Cregg et al., FEMS Microbiol. Rev. 24: 45-66 (2000)). However, glycosylated proteins expressed in P. pastoris generally contain additional mannose sugars resulting in “high mannose” glycans, as well as mannosylphosphate groups which impart a negative charge onto glycoproteins. Glycoproteins with either high mannose glycans or charged mannans present the risk of eliciting an unwanted immune response in humans (Takeuchi, Trends in Glycosci. Glycotechnol. 9:S29-S35 (1997); Rosenfeld and Ballou, J. Biol. Chem. 249: 2319-2321 (1974)). Accordingly, it is desirable to produce therapeutic glycoproteins in fungal host cells wherein the pattern of glycosylation on the glycoprotein is identical to or similar to that which occurs on glycoproteins produced in humans and which do not have detectable β-mannosylation.

As evidenced by the presence of protective antibodies in uninfected individuals, β-linked mannans are likely to be immunogenic or adversely affect the individual administered a therapeutic protein or glycoprotein comprising β-linked mannans. Additionally, exposed mannose groups on therapeutic proteins are rapidly cleared by mannose receptors on macrophage cells, resulting in low drug efficacy. Thus, the presence of β-linked mannose residues on N- or O-linked glycans of heterologous therapeutic proteins expressed in a fungal host, for example, P. pastoris, is not desirable given their immunogenic potential and their ability to bind to clearance factors.

Glycoproteins made in P. pastoris have been reported to contain β-linked mannose residues. In 2003, Trimble et al. (Glycobiol. 14: 265-274, Epub December 23) reported the presence of β-1,2-linked mannose residues in the recombinant human bile salt-stimulated lipase (hBSSL) expressed in P. pastoris. The genes encoding several β-mannosyltransferases have been identified in Pichia pastoris and Candida albicans (See U.S. Pat. No. 7,465,577 and Mille et al., J. Biol. Chem. 283: 9724-9736 (2008)).

In light of the above, there is a need to provide methods for making recombinant therapeutic proteins or glycoproteins in methylotrophic yeast such as Pichia pastoris that lack epitopes that might elicit an adverse reaction in an individual administered the recombinant therapeutic protein or glycoprotein. A method for determining whether a recombinant therapeutic protein or glycoprotein provides a risk of eliciting an adverse reaction when administered to an individual is to contact the recombinant therapeutic protein or glycoprotein to an antibody prepared against total host cell antigens. This is of particular concern for proteins or glycoproteins intended for chronic administration. The lack of cross binding to the antibody indicates that the recombinant therapeutic protein or glycoprotein lacks detectable cross binding activity to the antibody and is unlikely to elicit an adverse reaction when administered to an individual. Thus, there is a need for methods for producing a recombinant therapeutic protein or glycoprotein that lacks detectable cross binding activity to the antibody and is unlikely to elicit an adverse reaction when administered to an individual.

BRIEF SUMMARY OF THE INVENTION

The present invention provides methods for producing protein and glycoproteins in methylotrophic yeast such as Pichia pastoris that lack detectable cross binding activity to antibodies made against host cell antigens. In particular, the present invention provides methods using recombinant methylotrophic yeast such as Pichia pastoris strains, which do not display β-mannosyltransferase 2 activity with respect to an N-glycan or O-glycan and do not display at least one activity with respect to an N-glycan or O-glycan selected from β-mannosyltransferase 1, β-mannosyltransferase 3, and β-mannosyltransferase 4 to produce recombinant proteins and glycoproteins. In one aspect, the host cell is a Pichia pastoris strain in which the BMT2 gene encoding β-mannosyltransferase 2 and at least one gene encoding a β-mannosyltransferase selected from β-mannosyltransferase 1, 3, and 4 (genes BMT1, BMT3, BMT4, respectively) have been deleted or disrupted or mutated to produce an inactive β-mannosyltransferase to produce recombinant proteins and glycoproteins. In other aspects, the activity of one or more of the β-mannosyltransferase 1, β-mannosyltransferase 3, and β-mannosyltransferase 4 is abrogated using β-mannosyltransferase inhibitors which includes but is not limited to chemical compounds, antisense DNA to one or more mRNA encoding a β-mannosyltransferase, siRNA to one or more mRNA encoding a β-mannosyltransferase.

These recombinant Pichia pastoris strains can produce proteins and glycoproteins that lack detectable α-mannosidase resistant β-mannose residues thereon. The present invention further provides methods for producing bi-sialylated human erythropoietin in Pichia pastoris that lack detectable cross binding activity to antibodies against host cell antigens. The methods and host cells enable recombinant therapeutic proteins and glycoproteins to be produced that have a reduced risk of eliciting an adverse reaction in an individual administered the recombinant therapeutic proteins and glycoproteins compared to the same being produced in strains not modified as disclosed herein. The methods and host cells are also useful for producing recombinant proteins or glycoproteins that have a lower potential for binding clearance factors.

In one aspect, the present invention provides a recombinant methylotrophic yeast such as Pichia pastoris host cell that does not display β-mannosyltransferase 2 activity with respect to an N-glycan or O-glycan and does not display at least one activity with respect to an N-glycan or O-glycan selected from β-mannosyltransferase 1 activity and β-mannosyltransferase 3 activity and which includes a nucleic acid molecule encoding the recombinant glycoprotein. In further embodiments, the host cell does not display β-mannosyltransferase 2 activity, β-mannosyltransferase 1 activity, and β-mannosyltransferase 3 activity with respect to an N-glycan or O-glycan. In further embodiments, the host cell further does not display β-mannosyltransferase 4 activity with respect to an N-glycan or O-glycan.

In another aspect, the present invention provides a recombinant methylotrophic yeast such as Pichia pastoris host cell that has a deletion or disruption of the gene encoding β-mannosyltransferase 2 activity and a deletion or disruption of at least one gene selected a gene encoding a β-mannosyltransferase 1 activity and a β-mannosyltransferase 3 activity and which includes a nucleic acid molecule encoding the recombinant glycoprotein. In further embodiments, the host cell has a deletion or disruption of the genes encoding a β-mannosyltransferase 2 activity, a β-mannosyltransferase 1 activity, and a β-mannosyltransferase 3 activity. In further embodiments, the host cell has a deletion or disruption of the gene encoding a β-mannosyltransferase 4 activity.

In another aspect, the present invention provides a recombinant Pichia pastoris host cell in which the β-mannosyltransferase 2 (BMT2) gene and at least one gene selected from β-mannosyltransferase 1 (BMT1) and β-mannosyltransferase 3 (BMT3) has been deleted or disrupted and which includes a nucleic acid molecule encoding the recombinant protein or glycoprotein. In further embodiments, the β-mannosyltransferase 2 (BMT2), β-mannosyltransferase 1 (BMT1), and β-mannosyltransferase 3 (BMT3) genes are deleted. In further embodiments, the host cell further includes a deletion or disruption of the β-mannosyltransferase 4 (BMT4) gene.

In another aspect, the present invention provides a method for producing a recombinant glycoprotein in methylotrophic yeast such as Pichia pastoris that lacks detectable cross binding activity with antibodies made against host cell antigens, comprising providing a recombinant host cell that does not display a β-mannosyltransferase 2 activity with respect to an N-glycan or O-glycan and does not display at least one activity with respect to an N-glycan or O-glycan selected from β-mannosyltransferase 1 and β-mannosyltransferase 3 and which includes a nucleic acid molecule encoding the recombinant protein or glycoprotein; growing the host cell in a medium under conditions effective for expressing the recombinant glycoprotein; and recovering the recombinant glycoprotein from the medium to produce the recombinant glycoprotein that lacks detectable cross binding activity with antibodies made against host cell antigens. In further embodiments, the host cell does not display β-mannosyltransferase 2 activity, β-mannosyltransferase 1 activity, and β-mannosyltransferase 3 activity with respect to an N-glycan or O-glycan. In further embodiments, the host cell further does not display β-mannosyltransferase 4 activity with respect to an N-glycan or O-glycan.

In another aspect, the present invention provides a method for producing a recombinant glycoprotein in methylotrophic yeast such as Pichia pastoris that lacks detectable cross binding activity with antibodies made against host cell antigens, comprising providing a recombinant host cell that has a deletion or disruption of the gene encoding a β-mannosyltransferase 2 activity and a deletion or disruption of at least one gene encoding an activity selected from β-mannosyltransferase 1 activity and β-mannosyltransferase 3 activity and which includes a nucleic acid molecule encoding the recombinant protein or glycoprotein; growing the host cell in a medium under conditions effective for expressing the recombinant glycoprotein; and recovering the recombinant glycoprotein from the medium to produce the recombinant glycoprotein that lacks detectable cross binding activity with antibodies made against host cell antigens. In further embodiments, the host cell has a deletion or disruption of the genes encoding a β-mannosyltransferase 2 activity, a β-mannosyltransferase 1 activity, and a β-mannosyltransferase 3 activity. In further embodiments, the host cell has a deletion or disruption of the gene encoding a β-mannosyltransferase 4 activity.

In another aspect, the present invention provides a method for producing a recombinant glycoprotein in Pichia pastoris that lacks detectable cross binding activity with antibodies made against host cell antigens, comprising providing a recombinant Pichia pastoris host cell in which the β-mannosyltransferase 2 (BMT2) gene and at least one gene selected from β-mannosyltransferase 1 (BMT1) and β-mannosyltransferase 3 (BMT3) has been deleted or disrupted and which includes a nucleic acid molecule encoding the recombinant protein or glycoprotein; growing the host cell in a medium under conditions effective for expressing the recombinant glycoprotein; and recovering the recombinant glycoprotein from the medium to produce the recombinant glycoprotein that lacks detectable cross binding activity with antibodies made against host cell antigens. In further embodiments, the β-mannosyltransferase 2 (BMT2), β-mannosyltransferase 1 (BMT1), and β-mannosyltransferase 3 (BMT3) genes have been deleted or disrupted. In further embodiments, the host cell further includes a deletion or disruption of the β-mannosyltransferase (BMT4) gene.

In general, the detectable cross binding activity with antibodies made against host cell antigens is determined in an assay such as sandwich ELISA or a Western blot. The method is particularly useful for producing therapeutic proteins or glycoproteins. Examples of therapeutic proteins or glycoproteins include but are not limited to erythropoietin (EPO); cytokines such as interferon α, interferon β, interferon γ, and interferon ω; and granulocyte-colony stimulating factor (GCSF); GM-CSF; coagulation factors such as factor VIII, factor IX, and human protein C; antithrombin III; thrombin; soluble IgE receptor α-chain; immunoglobulins such as IgG, IgG fragments, IgG fusions, and IgM; immunoadhesions and other Fc fusion proteins such as soluble TNF receptor-Fc fusion proteins; RAGE-Fc fusion proteins; interleukins; urokinase; chymase; and urea trypsin inhibitor; IGF-binding protein; epidermal growth factor; growth hormone-releasing factor; annexin V fusion protein; angiostatin; vascular endothelial growth factor-2; myeloid progenitor inhibitory factor-1; osteoprotegerin; α-1-antitrypsin; α-feto proteins; DNase II; kringle 3 of human plasminogen; glucocerebrosidase; TNF binding protein 1; follicle stimulating hormone; cytotoxic T lymphocyte associated antigen 4—Ig; transmembrane activator and calcium modulator and cyclophilin ligand; glucagon like protein 1; and IL-2 receptor agonist

In particular embodiments of the host cell or method, the codons of the nucleic acid sequence of the nucleic acid molecule encoding the recombinant protein or glycoprotein is optimized for expression in Pichia pastoris.

In a further still embodiment of the host cell or method, the host cell is genetically engineered to produce glycoproteins that have human-like N-glycans.

In a further embodiment of the host cell or method, the host cell further does not display α1,6-mannosyltransferase activity with respect to the N-glycan on a glycoprotein and includes an α1,2-mannosidase catalytic domain fused to a cellular targeting signal peptide not normally associated with the catalytic domain and selected to target α1,2-mannosidase activity to the ER or Golgi apparatus of the host cell.

In a further still embodiment of the host cell or method, the host cell further includes a GlcNAc transferase I catalytic domain fused to a cellular targeting signal peptide not normally associated with the catalytic domain of and selected to target GlcNAc transferase I activity to the ER or Golgi apparatus of the host cell.

In a further still embodiment of the host cell or method, the host cell further includes a mannosidase II catalytic domain fused to a cellular targeting signal peptide not normally associated with the catalytic domain and selected to target mannosidase II activity to the ER or Golgi apparatus of the host cell.

In a further still embodiment of the host cell or method, the host cell further includes a GlcNAc transferase II catalytic domain fused to a cellular targeting signal peptide not normally associated with the catalytic domain and selected to target GlcNAc transferase II activity to the ER or Golgi apparatus of the host cell.

In a further still embodiment of the host cell or method the host cell further includes a galactosyltransferase catalytic domain fused to a cellular targeting signal peptide not normally associated with the catalytic domain and selected to target galactosyltransferase activity to the ER or Golgi apparatus of the host cell.

In a further still embodiment of the host cell or method, the host cell further includes a sialyltransferase catalytic domain fused to a cellular targeting signal peptide not normally associated with the catalytic domain and selected to target sialyltransferase activity to the ER or Golgi apparatus of the host cell.

In a further still embodiment of the host cell or method, the host cell further includes a fucosyltransferase catalytic domain fused to a cellular targeting signal peptide not normally associated with the catalytic domain and selected to target fucosyltransferase activity to the ER or Golgi apparatus of the host cell.

In a further still embodiment of the host cell or method, the host cell further includes one or more GlcNAc transferases selected from the group consisting of GnTIII, GnTIV, GnTV, GnTVI, and GnTIX.

In a further still embodiment of the host cell or method, the host cell is genetically engineered to produce glycoproteins that have predominantly an N-glycan selected from Man₅GlcNAc₂, GlcNAcMan₅GlcNAc₂, GalGlcNAcMan₅GlcNAc₂, NANAGalGlcNAcMan₅GlcNAc₂, GlcNAcMan₃GlcNAc₂, GlcNAc₍₁₋₄₎Man₃GlcNAc₂, Gal₍₁₋₄₎GlcNAc₍₁₋₄₎Man₃GlcNAc₂, and NANA₍₁₋₄₎Gal₍₁₋₄₎GlcNAc₍₁₋₄₎Man₃GlcNAc₂, wherein the subscript indicates the number of the particular sugar residues on the N-glycan structure. Examples of N-glycan structures include but are not limited to Man₅GlcNAc₂, GlcNAcMan₅GlcNAc₂, GlcNAcMan₃GlcNAc₂, GlcNAc₂Man₃GlcNAc₂, GlcNAc₃Man₃GlcNAc₂, GlcNAc₄Man₃GlcNAc₂, GalGlcNAc₂Man₃GlcNAc₂, Gal₂GlcNAc₂Man₃GlcNAc₂, Gal₂GlcNAc₃Man₃GlcNAc₂, Gal₂GlcNAc₄Man₃GlcNAc₂, Gal₃GlcNAc₃Man₃GlcNAc₂, Gal₃GlcNAc₄Man₃GlcNAc₂, Gal₄GlcNAc₄Man₃GlcNAc₂, NANAGal₂GlcNAc₂Man₃GlcNAc₂, NANA₂Gal₂GlcNAc₂Man₃GlcNAc₂, NANA₃Gal₃GlcNAc₃Man₃GlcNAc₂, and NANA₄Gal₄GlcNAc₄Man₃GlcNAc₂.

Further provided are compositions, which comprise one or more recombinant glycoproteins obtained by the above method using any one of the above host cells.

In a further aspect, the present invention provides a recombinant methylotrophic yeast such as Pichia pastoris host cell that does not display β-mannosyltransferase 2 activity and at least one activity selected from β-mannosyltransferase 1 activity and β-mannosyltransferase 3 activity and which includes two or more nucleic acid molecules, each encoding a fusion protein comprising a mature human erythropoietin fused to a signal peptide that targets the ER and which is removed when the fusion protein is in the ER. In particular embodiments, the host cell further does not display β-mannosyltransferase 4 activity.

In a further aspect, the present invention provides a recombinant methylotrophic yeast such as Pichia pastoris host cell that has a deletion or disruption of the genes encoding β-mannosyltransferase 2 activity, β-mannosyltransferase 1 activity, and β-mannosyltransferase 3 activity and which includes two or more nucleic acid molecules, each encoding a fusion protein comprising a mature human erythropoietin fused to a signal peptide that targets the ER and which is removed when the fusion protein is in the ER. In particular embodiments, the host cell further includes a deletion or disruption of the gene encoding β-mannosyltransferase 4 activity.

In a further aspect, the present invention provides a recombinant Pichia pastoris host cell that has a deletion or disruption of the β-mannosyltransferase 2 (BMT2) gene and at least one gene selected from a β-mannosyltransferase 1 (BMT1) and β-mannosyltransferase 3 (BMT3) gene and which includes two or more nucleic acid molecules, each encoding a fusion protein comprising a mature human erythropoietin fused to a signal peptide that targets the ER and which is removed when the fusion protein is in the ER. In particular embodiments, the host cell further includes a deletion or disruption of the gene encoding β-mannosyltransferase 4 (BMT4) gene.

In a further still aspect, the present invention provides a method for producing a mature human erythropoietin in methylotrophic yeast such as Pichia pastoris comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens, comprising: providing a recombinant host cell that does not display β-mannosyltransferase 2 activity with respect to an N-glycan or O-glycan and does not display at least one activity with respect to an N-glycan or O-glycan selected from β-mannosyltransferase 1 activity and β-mannosyltransferase 3 activity and is genetically engineered to produce sialic acid-terminated biantennary N-glycans and which includes two or more nucleic acid molecules, each encoding a fusion protein comprising a mature human erythropoietin fused to a signal peptide that targets the ER and which is removed when the fusion protein is in the ER; growing the host cell in a medium under conditions effective for expressing and processing the first and second fusion proteins; and recovering the mature human erythropoietin from the medium to produce the mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens. In further embodiments, the host cell does not display β-mannosyltransferase 2 activity, β-mannosyltransferase 1 activity, and β-mannosyltransferase 3 activity with respect to an N-glycan or O-glycan. In further embodiments, the host cell further does not display β-mannosyltransferase 4 activity.

In a further still aspect, the present invention provides a method for producing a mature human erythropoietin in methylotrophic yeast such as Pichia pastoris comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens, comprising: providing a recombinant host cell genetically engineered to produce sialic acid-terminated biantennary N-glycans and in which the gene encoding a β-mannosyltransferase 2 activity and at least one gene encoding an activity selected from a β-mannosyltransferase 1 activity and a β-mannosyltransferase 3 activity has been deleted or disrupted and which includes two or more nucleic acid molecules, each encoding a fusion protein comprising a mature human erythropoietin fused to a signal peptide that targets the ER and which is removed when the fusion protein is in the ER; growing the host cell in a medium under conditions effective for expressing and processing the first and second fusion proteins; and recovering the mature human erythropoietin from the medium to produce the mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens. In further embodiments, the host comprises a deletion or disruption of the genes encoding a β-mannosyltransferase 2 activity, a β-mannosyltransferase 1 activity, and a β-mannosyltransferase 3 activity have been deleted or disrupted. In further embodiments, the host cell further includes a deletion or disruption of a gene encoding a β-mannosyltransferase 3 activity.

In a further still aspect, the present invention provides a method for producing a mature human erythropoietin in Pichia pastoris comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens, comprising: providing a recombinant Pichia pastoris host cell genetically engineered to produce sialic acid-terminated biantennary N-glycans and in which the β-mannosyltransferase 2 (BMT2) gene and at least one gene selected from a β-mannosyltransferase 1 (BMT1) and β-mannosyltransferase 3 (BMT3) gene has been deleted or disrupted and which includes two or more nucleic acid molecules, each encoding a fusion protein comprising a mature human erythropoietin fused to a signal peptide that targets the ER and which is removed when the fusion protein is in the ER; growing the host cell in a medium under conditions effective for expressing and processing the first and second fusion proteins; and recovering the mature human erythropoietin from the medium to produce the mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens. In further embodiments, the host comprises a deletion or disruption of the β-mannosyltransferase 2 (BMT2) gene, β-mannosyltransferase 1 (BMT1) gene, and β-mannosyltransferase 3 (BMT3) gene have been deleted or disrupted. In further embodiments, the host cell further includes a deletion or disruption of a β-mannosyltransferase 3 gene (BMT4).

In particular embodiments of the host cell or method, the signal peptide fused to the N-terminus of the erythropoietin is a S. cerevisiae αMATpre signal peptide or a chicken lysozyme signal peptide.

In further embodiments of the host cell or method, at least one nucleic acid molecule encodes a fusion protein wherein the erythropoietin is fused to the S. cerevisiae αMATpre signal peptide and at least one nucleic acid molecule encodes a fusion protein wherein the erythropoietin is fused to the S. cerevisiae αMATpre signal peptide a chicken lysozyme signal peptide.

In further embodiments of the host cell or method, the codons of the nucleic acid sequence of the nucleic acid molecule encoding the erythropoietin is optimized for expression in Pichia pastoris.

In further embodiments of the method, recovering the mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens from the medium includes a cation exchange chromatography step.

In further embodiments of the method, recovering the mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens from the medium includes a hydroxyapatite chromatography step.

In further embodiments of the method, recovering the mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens from the medium includes an anion exchange chromatography step.

In further embodiments of the method, recovering the mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens from the medium includes a cation exchange chromatography step followed by a hydroxyapatite chromatography step, which is optionally followed by an anion exchange chromatography step.

The present invention further provides a composition comprising a mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens obtained from the above method using the above host cells and a pharmaceutically acceptable salt. In particular embodiments, about 50 to 60% of the N-glycans comprise sialic acid residues on both antennae; in further embodiments, greater than 70% of the N-glycans comprise sialic acid residues on both antennae; in further embodiments, greater than 80% of the N-glycans comprise sialic acid residues on both antennae. In further aspects, less than 30% of the N-glycans are neutral N-glycans (i.e., are not sialylated on at least one terminus at the non-reducing end of the N-glycan). In further still aspects, less than 20% of the N-glycans are neutral N-glycans. In particular aspects, about 99% of the N-glycans contain one ore more sialic acid residues and less than 1% of the N-glycans are neutral N-glycans. In further aspects, compositions are provided wherein there is 4.5 moles or more of sialic acid per mole of rhEPO. In further aspects, compositions are provided wherein there is at least 5.0 moles of sialic acid per mole of rhEPO.

In further embodiments of the composition, the mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens is conjugated to a hydrophilic polymer, which in particular aspects is a polyethylene glycol polymer. In particular embodiments, the polyethylene glycol polymer is conjugated to the N-terminus of the mature human erythropoietin comprising predominantly sialic acid-terminated bi-antennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens.

DEFINITIONS

As used herein, the terms “N-glycan” and “glycoform” are used interchangeably and refer to an N-linked oligosaccharide, e.g., one that is attached by an asparagine-N-acetylglucosamine linkage to an asparagine residue of a polypeptide. N-linked glycoproteins contain an N-acetylglucosamine residue linked to the amide nitrogen of an asparagine residue in the protein. The predominant sugars found on glycoproteins are glucose, galactose, mannose, fucose, N-acetylgalactosamine (GalNAc), N-acetylglucosamine (GlcNAc) and sialic acid (e.g., N-acetyl-neuraminic acid (NANA)). The processing of the sugar groups occurs co-translationally in the lumen of the ER and continues post-translationally in the Golgi apparatus for N-linked glycoproteins.

N-glycans have a common pentasaccharide core of Man₃GlcNAc₂ (“Man” refers to mannose; “Glc” refers to glucose; and “NAc” refers to N-acetyl; GlcNAc refers to N-acetylglucosamine). N-glycans differ with respect to the number of branches (antennae) comprising peripheral sugars (e.g., GlcNAc, galactose, fucose and sialic acid) that are added to the Man₃GlcNAc₂ (“Man3”) core structure which is also referred to as the “trimannose core”, the “pentasaccharide core” or the “paucimannose core”. N-glycans are classified according to their branched constituents (e.g., high mannose, complex or hybrid). A “high mannose” type N-glycan has five or more mannose residues. A “complex” type N-glycan typically has at least one GlcNAc attached to the 1,3 mannose arm and at least one GlcNAc attached to the 1,6 mannose arm of a “trimannose” core. Complex N-glycans may also have galactose (“Gal”) or N-acetylgalactosamine (“GalNAc”) residues that are optionally modified with sialic acid or derivatives (e.g., “NANA” or “NeuAc”, where “Neu” refers to neuraminic acid and “Ac” refers to acetyl). Complex N-glycans may also have intrachain substitutions comprising “bisecting” GlcNAc and core fucose (“Fuc”). Complex N-glycans may also have multiple antennae on the “trimannose core,” often referred to as “multiple antennary glycans.” A “hybrid” N-glycan has at least one GlcNAc on the terminal of the 1,3 mannose arm of the trimannose core and zero or more mannoses on the 1,6 mannose arm of the trimannose core. The various N-glycans are also referred to as “glycoforms.”

Abbreviations used herein are of common usage in the art, see, e.g., abbreviations of sugars, above. Other common abbreviations include “PNGase”, or “glycanase” or “glucosidase” which all refer to peptide N-glycosidase F (EC 3.2.2.18).

The term “recombinant host cell” (“expression host cell”, “expression host system”, “expression system” or simply “host cell”), as used herein, is intended to refer to a cell into which a recombinant vector has been introduced. It should be understood that such terms are intended to refer not only to the particular subject cell but to the progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term “host cell” as used herein. A recombinant host cell may be an isolated cell or cell line grown in culture or may be a cell which resides in a living tissue or organism. Preferred host cells are yeasts and fungi.

A host cell that “does not display” an enzyme activity refers to a host cell in which the enzyme activity has been abrogated or disrupted. For example, the enzyme activity can be abrogated or disrupted by deleting or disrupting the gene encoding the enzyme activity (included deleting or disrupting the upstream or downstream regulatory sequences controlling expression of the gene; the enzyme activity can be abrogated or disrupted by mutating the gene encoding the enzyme activity to render the enzyme activity encoded gene non-functional; the enzyme activity can be abrogated or disrupted by use of a chemical, peptide, or protein inhibitor of the enzyme activity; the enzyme activity can be abrogated or disrupted by use of nucleic acid-based expression inhibitors such as antisense DNA and siRNA; and, the enzyme activity can be abrogated or disrupted by use of transcription inhibitors or inhibitors of the expression or activity of regulatory factors that control or regulate expression of the gene encoding the enzyme activity.

When referring to “mole percent” of a glycan present in a preparation of a glycoprotein, the term means the molar percent of a particular glycan present in the pool of N-linked oligosaccharides released when the protein preparation is treated with PNG'ase and then quantified by a method that is not affected by glycoform composition, (for instance, labeling a PNG'ase released glycan pool with a fluorescent tag such as 2-aminobenzamide and then separating by high performance liquid chromatography or capillary electrophoresis and then quantifying glycans by fluorescence intensity). For example, 50 mole percent NANA₂Gal₂GlcNAc₂Man₃GlcNAc₂ means that 50 percent of the released glycans are NANA₂Gal₂GlcNAc₂Man₃GlcNAc₂ and the remaining 50 percent are comprised of other N-linked oligosaccharides. In embodiments, the mole percent of a particular glycan in a preparation of glycoprotein will be between 20% and 100%, preferably above 25%, 30%, 35%, 40% or 45%, more preferably above 50%, 55%, 60%, 65% or 70% and most preferably above 75%, 80% 85%, 90% or 95%.

As used herein, the term “predominantly” or variations such as “the predominant” or “which is predominant” will be understood to mean the glycan species that has the highest mole percent (%) of total N-glycans after the glycoprotein has been treated with PNGase and released glycans analyzed by mass spectroscopy, for example, MALDI-TOF MS. In other words, the phrase “predominantly” is defined as an individual entity, such as a specific glycoform, is present in greater mole percent than any other individual entity. For example, if a composition consists of species A in 40 mole percent, species B in 35 mole percent and species C in 25 mole percent, the composition comprises predominantly species A.

The term “therapeutically effective amount” refers to an amount of the recombinant erythropoietin of the invention which gives an increase in hematocrit that provides benefit to a patient. The amount will vary from one individual to another and will depend upon a number of factors, including the overall physical condition of the patient and the underlying cause of anemia. For example, a therapeutically effective amount of erythropoietin of the present invention for a patient suffering from chronic renal failure can be in the range of 20 to 300 units/kg or 0.5 ug/kg to 500 ug/kg based on therapeutic indication. The term “unit” refers to units commonly known in the art for assessing the activity of erythropoietin compositions. A milligram of pure erythropoietin is approximately equivalent to 150,000 units. A dosing schedule can be from about three times per week to about once every four or six weeks. The actual schedule will depend on a number of factors including the type of erythropoietin administered to a patient (EPO or PEGylated-EPO) and the response of the individual patient. The higher dose ranges are not typically used in anemia applications but can be useful on other therapeutic applications. The means of achieving and establishing an appropriate dose of erythropoietin for a patient is well known and commonly practiced in the art.

Variations in the amount given and dosing schedule from patient to patient are including by reference to the term “about” in conjunction with an amount or schedule. The amount of erythropoietin used for therapy gives an acceptable rate of hematocrit increase and maintains the hematocrit at a beneficial level (for example, usually at least about 30% and typically in a range of 30% to 36%). A therapeutically effective amount of the present compositions may be readily ascertained by one skilled in the art using publicly available materials and procedures. Additionally, iron may be given to the patient to maintain increased erythropoiesis during therapy. The amount to be given may be readily determined by methods commonly used by those skilled in the art.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A-J shows the genealogy of P. pastoris strain YGLY3159 (FIG. 1E) and strains YGLY7113 to YGLY7122 (FIG. 11) beginning from wild-type strain NRRL-Y11430 (FIG. 1A).

FIG. 2 shows a map of plasmid pGLY6. Plasmid pGLY6 is an integration vector that targets the URA5 locus and contains a nucleic acid molecule comprising the S. cerevisiae invertase gene or transcription unit (ScSUC2) flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region of the P. pastoris URA5 gene (PpURAS-5′) and on the other side by a nucleic acid molecule comprising the a nucleotide sequence from the 3′ region of the P. pastoris URA5 gene (PpURAS-3′).

FIG. 3 shows a map of plasmidpGLY40. Plasmid pGLY40 is an integration vector that targets the OCH1 locus and contains a nucleic acid molecule comprising the P. pastoris URA5 gene or transcription unit (PpURAS) flanked by nucleic acid molecules comprising lacZ repeats (lacZ repeat) which in turn is flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region of the OCH1 gene (PpOCH1-5′) and on the other side by a nucleic acid molecule comprising a nucleotide sequence from the 3′ region of the OCH1 gene (PpOCH1-3′).

FIG. 4 shows a map of plasmid pGLY43a. Plasmid pGLY43a is an integration vector that targets the BMT2 locus and contains a nucleic acid molecule comprising the K. lactis UDP-N-acetylglucosamine (UDP-GlcNAc) transporter gene or transcription unit (KlGlcNAc Transp.) adjacent to a nucleic acid molecule comprising the P. pastoris URA5 gene or transcription unit (PpURAS) flanked by nucleic acid molecules comprising lacZ repeats (lacZ repeat). The adjacent genes are flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region of the BMT2 gene (PpPBS2-5′) and on the other side by a nucleic acid molecule comprising a nucleotide sequence from the 3′ region of the BMT2 gene (PpPBS2-3′).

FIG. 5 shows a map of plasmid pGLY48. Plasmid pGLY48 is an integration vector that targets the MNN4L1 locus and contains an expression cassette comprising a nucleic acid molecule encoding the mouse homologue of the UDP-GlcNAc transporter (MmGlcNAc Transp.) open reading frame (ORF) operably linked at the 5′ end to a nucleic acid molecule comprising the P. pastoris GAPDH promoter (PpGAPDH Prom) and at the 3′ end to a nucleic acid molecule comprising the S. cerevisiae CYC termination sequence (ScCYCTT) adjacent to a nucleic acid molecule comprising the P. pastoris URA5 gene or transcription unit (PpURAS) flanked by lacZ repeats (lacZ repeat) and in which the expression cassettes together are flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region of the P. Pastoris MNN4L1 gene (PpMNN4L1-5′) and on the other side by a nucleic acid molecule comprising a nucleotide sequence from the 3′ region of the MNN4L1 gene (PpMNN4L1-3′).

FIG. 6 shows as map of plasmid pGLY45. Plasmid pGLY45 is an integration vector that targets the PNO1/MNN4 loci contains a nucleic acid molecule comprising the P. pastoris URA5 gene or transcription unit (PpURAS) flanked by nucleic acid molecules comprising lacZ repeats (lacZ repeat) which in turn is flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region of the PNO1 gene (PpPNO1-5′) and on the other side by a nucleic acid molecule comprising a nucleotide sequence from the 3′ region of the MNN4 gene (PpMNN4-3′).

FIG. 7 shows a map of plasmid pGLY247. Plasmid pGLY247 is an integration vector that targets the MET16 locus and contains a nucleic acid molecule comprising the P. pastoris URA5 gene or transcription unit (PpURAS) flanked by nucleic acid molecules comprising lacZ repeats (lacZ repeat) which in turn is flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region of the MET16 gene (PpMET16-5′) and on the other side by a nucleic acid molecule comprising a nucleotide sequence from the 3′ region of the MET16 gene (PpMET16-3′).

FIG. 8 shows a map of plasmid pGLY248. Plasmid pGLY248 is an integration vector that targets the URA5 locus and contains a nucleic acid molecule comprising the P. pastoris MET16 gene or transcription unit (PpMET16) flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region of the URA5 gene (PpURAS-5′) and on the other side by a nucleic acid molecule comprising a nucleotide sequence from the 3′ region of the URA5 gene (PpURA5-3′).

FIG. 9 shows a map of plasmid pGLY582. Plasmid pGLY582 is an integration vector that targets the HIS1 locus and contains in tandem four expression cassettes encoding (1) the S. cerevisiae UDP-glucose epimerase (ScGAL10), (2) the human galactosyltransferase I (hGalT) catalytic domain fused at the N-terminus to the S. cerevisiae KRE2-s leader peptide (33), (3) the P. pastoris URA5 gene or transcription unit (PpURAS) flanked by lacZ repeats (lacZ repeat), and (4) the D. melanogaster UDP-galactose transporter (DmUGT). All flanked by the 5′ region of the HIS1 gene (PpHIS1-5′) and the 3′ region of the HIS1 gene (PpHIS1-3′). PMA1 is the P. pastoris PMA1 promoter; PpPMA1 TT is the P. pastoris PMA1 termination sequence; GAPDH is the P. pastoris GADPH promoter and ScCYC TT is the S. cerevisiae CYC termination sequence; PpOCH1 Prom is the P. pastoris OCH1 promoter and PpALG12 TT is the P. pastoris ALG12 termination sequence.

FIG. 10 shows a map of plasmid pGLY167b. Plasmid pGLY167b is an integration vector that targets the ARG1 locus and contains in tandem three expression cassettes encoding (1) the D. melanogaster mannosidase II catalytic domain (codon optimized) fused at the N-terminus to S. cerevisiae MNN2 leader peptide (CO-KD53), (2) the P. pastoris HIS1 gene or transcription unit, and (3) the rat N-acetylglucosamine (GlcNAc) transferase II catalytic domain (codon optimized) fused at the N-terminus to S. cerevisiae MNN2 leader peptide (CO-TC54). All flanked by the 5′ region of the ARG1 gene (PpARG1-5′) and the 3′ region of the ARG1 gene (PpARG1-3′). PpPMA1 prom is the P. pastoris PMA1 promoter; PpPMA1 TT is the P. pastoris PMA1 termination sequence; PpGAPDH is the P. pastoris GADPH promoter; ScCYC TT is the S. cerevisiae CYC termination sequence; PpOCH1 Prom is the P. pastoris OCH1 promoter; and PpALG12 TT is the P. pastoris ALG12 termination sequence.

FIG. 11 shows a map of plasmid pGLY1430. Plasmid pGLY1430 is a KINKO integration vector that targets the ADE1 locus without disrupting expression of the locus and contains in tandem four expression cassettes encoding (1) the human GlcNAc transferase I catalytic domain (codon optimized) fused at the N-terminus to P. pastoris SEC12 leader peptide (CO-NA10), (2) mouse homologue of the UDP-GlcNAc transporter (MmTr), (3) the mouse mannosidase IA catalytic domain (FB) fused at the N-terminus to S. cerevisiae SEC12 leader peptide (FB8), and (4) the P. pastoris URA5 gene or transcription unit (PpURAS) flanked by lacZ repeats (lacZ). All flanked by the 5′ region of the ADE1 gene and ORF (ADE1 5′ and ORF) and the 3′ region of the ADE1 gene (PpADE1-3′). PpPMA1 prom is the P. pastoris PMA1 promoter; PpPMA1 TT is the P. pastoris PMA1 termination sequence; SEC4 is the P. pastoris SEC4 promoter; OCH1 TT is the P. pastoris OCH1 termination sequence; ScCYC TT is the S. cerevisiae CYC termination sequence; PpOCH1 Prom is the P. pastoris OCH1 promoter; PpALG3 TT is the P. pastoris ALG3 termination sequence; and PpGAPDH is the P. pastoris GADPH promoter.

FIG. 12 shows a map of plasmid pGFI165. Plasmid pGFI165 is a KINKO integration vector that targets the PRO1 locus without disrupting expression of the locus and contains expression cassettes encoding (1) the T. reesei α-1,2-mannosidase catalytic domain fused at the N-terminus to S. cerevisiae αMATpre signal peptide (aMATTrMan) to target the chimeric protein to the secretory pathway and secretion from the cell and (2) the P. pastoris URA5 gene or transcription unit flanked by lacZ repeats (lacZ repeat). All flanked by the 5′ region of the PRO1 gene and ORF (5′PRO1orf) and the 3′ region of the PRO1 gene (3′PRO). ScCYC TT is the S. cerevisiae CYC termination sequence; PpALG3 TT is the P. pastoris ALG3 termination sequence; and PpGAPDH is the P. pastoris GADPH promoter.

FIG. 13 shows a map of plasmid pGLY2088. Plasmid pGLY2088 is an integration vector that targets the TRP2 or AOX1 locus and contains expression cassettes encoding (1) mature human erythropoetin (co-hEPO) codon optimized fused at the N-terminus to a S. cerevisiae αMATpre signal peptide (alpha MF-pre) to target the chimeric protein to the secretory pathway and secretion from the cell and (2) the zeocin resistance protein (ZeocinR). The cassettes are flanked on one end with the P. pastoris AOX1 promoter (PpAOX1 Prom) and on the other end with the P. pastoris TRP2 gene or transcription unit (PpTRP2). ScCYC TT is the S. cerevisiae CYC termination sequence and ScTEF Prom is the S. cerevisiae TEF1 promoter.

FIG. 14 shows a map of plasmid pGLY2456. Plasmid pGLY2456 is a KINKO integration vector that targets the TRP2 locus without disrupting expression of the locus and contains six expression cassettes encoding (1) the mouse CMP-sialic acid transporter codon optimized (CO mCMP-Sia Transp), (2) the human UDP-GlcNAc 2-epimerase/N-acetylmannosamine kinase codon optimized (CO hGNE), (3) the Pichia pastoris ARG1 gene or transcription unit, (4) the human CMP-sialic acid synthase codon optimized (CO hCMP-NANA S), (5) the human N-acetylneuraminate-9-phosphate synthase codon optimized (CO hSIAP S), and, (6) the mouse a-2,6-sialyltransferase catalytic domain codon optimized fused at the N-terminus to S. cerevisiae KRE2 leader peptide (comST6-33). All flanked by the 5′ region of the TRP2 gene and ORF (PpTRP2 5′) and the 3′ region of the TRP2 gene (PpTRP2-3′). PpPMA1 prom is the P. pastoris PMA1 promoter; PpPMA1 TT is the P. pastoris PMA1 termination sequence; CYC TT is the S. cerevisiae CYC termination sequence; PpTEF Prom is the P. pastoris TEF1 promoter; PpTEF TT is the P. pastoris TEF1 termination sequence; PpALG3 TT is the P. pastoris ALG3 termination sequence; and pGAP is the P. pastoris GAPDH promoter.

FIG. 15 shows a map of plasmid pGLY3411 (pSH1092). Plasmid pGLY3411 (pSH1092) is an integration vector that contains the expression cassette comprising the P. pastoris URA5 gene or transcription unit (PpURA5) flanked by lacZ repeats (lacZ repeat) flanked on one side with the 5′ nucleotide sequence of the P. pastoris BMT4 gene (PpPBS4 5′) and on the other side with the 3′ nucleotide sequence of the P. pastoris BMT4 gene (PpPBS4 3′).

FIG. 16 shows a map of plasmid pGLY3430 (pSH1115). Plasmid pGLY3430 (pSH1115) is an integration vector that contains an expression cassette comprising a nucleic acid molecule encoding the Nourseothricin resistance ORF (NAT) operably linked to the Ashbya gossypii TEF1 promoter (PTEF) and Ashbya gossypii TEF1 termination sequence (TTEF) flanked one side with the 5′ nucleotide sequence of the P. pastoris BMT1 gene (PBS1 5′) and on the other side with the 3′ nucleotide sequence of the P. pastoris BMT1 gene (PBS1 3′).

FIG. 17 shows a map of plasmid pGLY4472 (pSH1186). Plasmid pGLY4472 (pSH1186) contains an expression cassette comprising a nucleic acid molecule encoding the E. coli hygromycin B phosphotransferase gene ORF (Hyg) operably linked to the Ashbya gossypii TEF1 promoter (pTEF) and Ashbya gossypii TEF1 termination sequence (TRFtt) flanked one side with the 5′ nucleotide sequence of the P. pastoris BMT3 gene (PpPBS3 5′) and on the other side with the 3′ nucleotide sequence of the P. pastoris BMT3 gene (PpPBS3 3′).

FIG. 18 shows a map of plasmid pGLY2057. Plasmid pGLY2057 is an integration plasmid that targets the ADE2 locus and contains an expression cassette encoding the P. pastoris URA5 gene or transcription unit (PpURAS) flanked by lacZ repeats (lacZ repeat). The expression cassette is flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region of the ADE2 gene (PpADE2-5′) and on the other side by a nucleic acid molecule comprising a nucleotide sequence from the 3′ region of the ADE2 gene (PpADE2-3′).

FIG. 19 shows a map of plasmid pGLY2680. Plasmid pGLY2680 is an integration vector that can target the TRP2 or AOX1 locus and contains expression cassettes encoding (1) the human mature erythropoetin codon optimized (co-hEPO) fused at the N-terminus to chicken lysozyme signal peptide (chicken Lysozyme ss) and (2) the P. pastoris ADE2 gene without a promoter (PpADE2). The cassettes are flanked on one end with the P. pastoris AOX1 promoter (PpAOX1 Prom) and on the other end with the P. pastoris TRP2 gene or transcription unit (PpTRP2). ScCYC TT is the S. cerevisiae CYC termination sequence.

FIG. 20 shows a map of plasmid pGLY2713. Plasmid pGLY2713 is an integration vector containing the P. pastoris PNO1 ORF (PpPNO1 ORF) adjacent to the expression cassette comprising the P. pastoris URA5 gene or transcription unit (PpURAS) flanked by lacZ repeats (lacZ repeat) and flanked on one side with the 5′ nucleotide sequence of the P. pastoris PEP4 gene (PpPEP4 5′) and on the other side with the 3′ nucleotide sequence of the P. pastoris PEP4 gene (PpPEP4 3′).

FIG. 21 shows a schematic diagram illustrating fermentation process flow.

FIG. 22 shows that rhEPO produced in strain YGLY3159 has cross binding activity to anti-HCA antibodies. Left panel shows a Commassie Blue stained 4-20% SDS-PAGE gel showing the position of the rhEPO and right panel shows a Western blot of a similar gel probed with rabbit anti-HCA antibodies (SL rProA purified rabbit: 9161) at 1:3,000 dilution. Bound anti-HCA antibody was detected using goat anti-rabbit antibody conjugated to horseradish peroxidase (HRP) at a 1:5,000 dilution in PBS. Detection of bound secondary antibody used the substrate 3′3 diaminobenzidine (DAB).

FIG. 23 shows that the cross-bind activity of the rhEPO produced in strain YGLY3159 to anti-HCA antibodies is not detected when the rhEPO is deglycosylated using PNAGase F. Left panel shows a Commassie Blue stained 4-20% SDS-PAGE gel showing the position of the glycosylated and deglycosylated forms of rhEPO and right panel shows a Western blot of a similar gel probed with anti-HCA antibodies as in FIG. 22.

FIG. 24 shows that a recombinant antibody (rhIgG) produced in wild-type P. pastoris and a glycoengineered P. pastoris GS2.0 strain in which the BMT2 gene has been disrupted or deleted showed cross binding activity to anti-HCA antibodies. Left panel shows a Commassie Blue stained 4-20% SDS-PAGE gel and the right panel shows a Western blot of a similar gel probed with anti-HCA antibodies as in FIG. 22. GS 2.0 is a P. pastoris strain that produces glycoproteins that have predominantly Man₅GlcNAc₂ N-glycans. The shown GS 2.0 strain produced rhIgG with about 5% Man₉GlcNAc₂ N-glycans. WT is wild type P. pastoris.

FIG. 25 compares cross binding activity of rhEPO produced in strain YGLY3159 to other glycosylated proteins containing complex glycosylation patterns but not produced in P. pastoris to anti-HCA antibody. Upper panel shows a Commassie Blue stained 4-20% SDS-PAGE gel showing the position of the glycosylated and deglycosylated forms of rhEPO produced in P. pastoris and of recombinant human fetuin, asialofetuin (human fetuin with terminal sialic acid residues removed), human serum albumin (HSA), and recombinant LEUKINE produced in S. cerevisiae and the lower panel shows a Western blot of a similar gel probed with anti-HCA antibodies as in FIG. 22. S30S pools are rhEPO purified by cation exchange chromatography.

FIG. 26 shows that rhEPO produced in strain YGLY3159 and purified by hydroxyapatite chromatography still has cross binding activity to anti-HCA antibodies. Left panel shows a Commassie Blue stained 4-20% SDS-PAGE gel of chromatography elution pools 1, 2, and 3 showing the position of the rhEPO (reduced or non-reduced) and right panel shows a Western blot of a similar gel probed with anti-HCA antibodies as in FIG. 22. Below the panels is shown the results of an HPLC analysis of N-glycans in pools 1, 2, and 3.

FIG. 27A shows a chromatogram of Q SEPHAROSE FF anion chromatography purification of rhEPO produced in strain YGLY3159 from hydroxyapatite pool 1.

FIG. 27B shows a sandwich ELISA showing that the Q SEPHAROSE FF pool containing rhEPO from the Q SEPHAROSE FF anion chromatography has no detectable cross binding activity to anti-HCA antibodies whereas the flow through contained cross binding activity to anti-HCA antibodies. The capture antibody was anti-hEPO antibody and cross binding activity was detected with rabbit anti-HCA antibody at a 1:800 starting dilution in PBS which was then serially diluted 1:1 in PBS across a row ending with the 11^(th) well at a 1:819, 200 dilution (well 12: negative control). Bound anti-HCA antibody was detected using goat anti-rabbit antibody conjugated to alkaline phosphatase (AP) at a 1:10,000 dilution in PBS. Detection of bound secondary antibody used the substrate 4-Methylumbelliferyl phosphate (4-MUPS).

FIG. 28 shows that rhEPO produced in strains YGLY6661 (Δbmt2, Δbmt4, and Δbmt1) and YGLY7013 (Δbmt2 and Δbmt4) and captured by Blue SEPHAROSE 6 FF chromatography (Blue pools) still has cross binding activity to anti-HCA antibodies. Left panel shows a Commassie Blue stained 4-20% SDS-PAGE gel of the Blue pools with (+) and without (−) PNGase F treatment. The center panel shows a Western blot of a similar gel probed with anti-hEPO antibodies conjugated to HRP at a 1:1,000 dilution and DAB as the substrate. The right panel shows a Western blot of a similar gel probed with anti-HCA antibodies as in FIG. 22.

FIG. 29 shows in a sandwich ELISA to detect cross binding activity to anti-HCA antibodies that rhEPO produced in strains YGLY6661 (Δbmt2, Δbmt4, and Δbmt1) and YGLY7013 (Δbmt2 and Δbmt4) and captured by Blue SEPHAROSE 6 FF chromatography (Blue pools) still has cross binding activity to anti-HCA antibodies. The ELISA was performed as in FIG. 27B.

FIG. 30 shows sandwich ELISAs used to detect cross binding activity to anti-HCA antibodies of rhEPO produced in strains YGLY6661 (Δbmt2, Δbmt4, and Δbmt1) and YGLY7013 (Δbmt2 and Δbmt4), captured by Blue SEPHAROSE 6 FF chromatography, and purified by hydroxyapatite chromatography (HA pool 1). rhEPO in HA pool 1 from strain YGLY6661 had no detectable cross binding activity to anti-HCA antibodies. The ELISAs were performed as in FIG. 27B.

FIG. 31 shows that rhEPO produced in strain YGLY6661 (Δbmt2, Δbmt4, and Δbmt1) and captured by Blue SEPHAROSE 6 FF chromatography (Blue pools) still has cross binding activity to anti-HCA antibodies. Left panel shows a Commassie Blue stained 4-20% SDS-PAGE gel of the Blue pools with (+) and without (−) PNGase F treatment. The center panel shows a Western blot of a similar gel probed with anti-hEPO antibodies conjugated to HRP at a 1:1,000 dilution and DAB as the substrate. The right panel shows a Western blot of a similar gel probed with anti-HCA antibodies as in FIG. 22.

FIG. 32A shows a Commassie Blue stained 4-20% SDS-PAGE gel of the Blue Sepaharose 6 FF capture pools (Blue pools) prepared from strains YGLY7361-7366 (all Δbmt2, Δbmt4, Δbmt1, and Δbmt3) with (+) and without (−) PNGase F treatment. The strains were grown in 500 mL SixFors fermentors.

FIG. 32B shows a Commassie Blue stained 4-20% SDS-PAGE gel of the Blue Sepaharose 6 FF capture pools (Blue pools) prepared from strains YGLY7393-7398 (all Δbmt2, Δbmt4, Δbmt1, and Δbmt3) with (+) and without (−) PNGase F treatment. The strains were grown in 500 mL SixFors fermentors.

FIG. 33 shows the results of sandwich ELISAs used to detect cross binding activity to anti-HCA antibodies of rhEPO produced in strains YGLY7361-7366 (all Δbmt2, Δbmt4, Δbmt1, and Δbmt3) and YGLY7393-7398 (all Δbmt2, Δbmt4, Δbmt1, and Δbmt3) and captured by Blue SEPHAROSE 6 FF chromatography (Blue pools). Only rhEPO in the Blue pools from strain YGLY7363 and YGLY7365 had detectable cross binding activity to anti-HCA antibodies. The ELISAs were performed as in FIG. 27B.

FIG. 34 shows in chart form the results from HPLC analysis of the N-glycans on the rhEPO in the Blue pools prepared from strains YGLY7361-7366 and YGLY7393-7398 (all Δbmt2, Δbmt4, Δbmt1, and Δbmt3). “Bi” refers to N-glycans in which both arms of the biantennary N-glycan are sialylated. “Mono” refers to N-glycans in which only one arm of the biantennary N-glycan is sialylated. “Neutral” refers to N-glycans that are not sialylated.

FIG. 35A shows a Commassie Blue stained 4-20% SDS-PAGE gel of the Blue SEPHAROSE 6 FF chromatography (Blue pools) and hydroxyapatite purification pools (HA pool 1s) prepared from strains YGLY7362, YGLY7366, YGLY7396, and YGLY7398 (all Δbmt2, Δbmt4, Δbmt1, and Δbmt3), and YGLY3159 (Δbmt2).

FIG. 35B shows a Western blot of a 4-20% SDS-PAGE gel of the Blue SEPHAROSE 6 FF chromatography (Blue pools) and hydroxyapatite purification pools (HA pool 1s) prepared from strains YGLY7362, YGLY7366, YGLY7396, and YGLY7398 (all Δbmt2, Δbmt4, Δbmt1, and Δbmt3), and YGLY3159 (Δbmt2) and probed with anti-HCA antibodies as in FIG. 22.

FIG. 36 shows that rhEPO produced in strain YGLY7398 (Δbmt2, Δbmt4, Δbmt1, and Δbmt3) and captured by Blue SEPHAROSE 6 FF chromatography (Blue pools) and purified by hydroxyapatite chromatography (HA pool 1s) had no detectable cross binding activity to anti-HCA antibodies. Left panel shows a Commassie Blue stained 4-20% SDS-PAGE gel of the Blue pool and HA pool 1 prepared from strain YGLY7398 compared to rhEPO prepared from strain YGLY3159. The center panel shows a Western blot of a similar gel probed with anti-HCA antibodies as in FIG. 22. The center panel shows a Western blot of a similar gel probed with anti-HCA antibodies as in FIG. 22 except anti-HCA antibodies were from another antibody preparation (GiF polyclonal rabbit::6316 at 1:2,000).

FIG. 37 shows the results of sandwich ELISAs used to detect cross binding activity to anti-HCA antibodies of rhEPO produced in strains YGLY7113-7122 (Δbmt2, Δbmt4, Δbmt1, and Δbmt3) and captured by Blue SEPHAROSE 6 FF chromatography (Blue pools). Strain YGLY7118 showed very low detectable cross binding activity to anti-HCA antibodies. None of the other strains showed any detectable cross binding activity to anti-HCA antibodies. The ELISAs were performed as in FIG. 27B.

FIG. 38 shows in chart form the results from HPLC analysis of the N-glycans on the rhEPO in the Blue pools prepared from strains YGLY7113-7122 (all Δbmt2, Δbmt4, Δbmt1, and Δbmt3). “Bi” refers to N-glycans in which both arms of the biantennary N-glycan are sialylated. “Mono” refers to N-glycans in which only one arm of the biantennary N-glycan is sialylated. “Neutral” refers to N-glycans that are not sialylated.

FIG. 39A shows a Commassie Blue stained 4-20% SDS-PAGE gel of the Blue SEPHAROSE 6 FF chromatography (Blue pools) and hydroxyapatite purification pools (HA pool 1s) prepared from strains YGLY7115, YGLY7117, YGLY7394, YGLY7395, and YGLY7120 (all Δbmt2, Δbmt4, Δbmt1, and Δbmt3), and YGLY3159 (Δbmt2).

FIG. 39B shows a Western blot of a 4-20% SDS-PAGE gel of the Blue SEPHAROSE 6 FF chromatography (Blue pools) and hydroxyapatite purification pools (HA pool 1s) prepared from strains YGLY7115, YGLY7117, YGLY7394, YGLY7395, and YGLY7120 (all Δbmt2, Δbmt4, Δbmt1, and Δbmt3), and YGLY3159 (Δbmt2) and probed with anti-HCA antibodies as in FIG. 22.

FIG. 40A shows an HPLC trace of the N-glycans from rhEPO produced in YGLY3159 (Δbmt2) and purified by hydroxyapatite column chromatography (i.e., analysis of HA pool 1).

FIG. 40B shows an HPLC trace of the N-glycans from rhEPO produced in YGLY7117 (Δbmt2, Δbmt4, Δbmt1, and Δbmt3) and purified by hydroxyapatite column chromatography (i.e., analysis of HA pool 1).

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides methods for producing proteins and glycoproteins in methylotrophic yeast such as Pichia pastoris that lack detectable cross binding to antibodies made against host cell antigens. Host cell antigens can also include residual host cell protein and cell wall contaminants that may carry over to recombinant protein compositions that can be immunogenic and which can alter therapeutic efficacy or safety of a therapeutic protein. A composition that has cross-reactivity with antibodies made against host cell antigens means that the composition contains some contaminating host cell material, usually N-glycans with phosphomannose residues or β-mannose residues or the like. Wild-type strains of Pichia pastoris will produce glycoproteins that have these N-glycan structures. Antibody preparations made against total host cell proteins would be expected to include antibodies against these structures. Proteins that do not contain N-glycans, however, might also include contaminating material (proteins or the like) that will cross-react with antibodies made against the host cell.

The methods and host cells enable recombinant therapeutic proteins and glycoproteins to be produced that have a reduced risk of eliciting an adverse reaction in an individual administered the recombinant therapeutic proteins and glycoproteins compared to the same being produced in strains not modified as disclosed herein. An adverse reaction includes eliciting an unwanted immune response in the individual or an unwanted or inappropriate binding to, congregating in, or interaction with a site in the individual that in general adversely affects the health of the individual. The risk of eliciting an adverse reaction in an individual being administered the therapeutic protein or glycoprotein is of particular concern for proteins or glycoproteins intended to be administered to the individual chronically (e.g., therapies intended to be conducted over an extended time period). The recombinant therapeutic proteins or glycoproteins produced according to the methods herein have no detectable cross binding activity to antibodies against host cell antigens and thus, present a reduced risk of eliciting an adverse reaction in an individual administered the recombinant proteins or glycoproteins. The methods and host cells are also useful for producing recombinant proteins or glycoproteins that have a lower potential for binding clearance factors.

The inventors have found that particular glycoproteins that are produced in some strains of Pichia pastoris can have N- or O-glycans thereon in which one or more of the mannose residues thereon are in a β1,2-linkage. Glycoproteins intended for therapeutic uses and which have one or more β1,2-linked mannose residues thereon provide a risk of being capable of eliciting an undesirable immune response in the individual being administered the glycoprotein. These β-linked mannose residues can be detected using antibodies made against total host cell antigens. Because it cannot be predicted which therapeutic glycoproteins will have N- or O-glycans comprising one or more β1,2-linked mannose residues and whether a therapeutic glycoprotein that does have N- or O-glycans comprising β1,2-linked mannose residues thereon will produce an unwanted immunogenic response in the individual receiving the glycoprotein, it is desirable to produce therapeutic glycoproteins in Pichia pastoris strains that have been genetically engineered to that lack detectable cross binding to antibodies made against host cell antigens. Such strains can be produced by deleting or disrupting the activities of at least three of the four known β-mannosyltransferases (Bmtp) in the Pichia pastoris β-mannosyltransferase (BMT) gene family. As shown herein, Pichia pastoris strains that include a deletion or disruption of at least three of the these BMT genes provides a Pichia pastoris strain that can produce proteins or glycoproteins that lack detectable cross binding to antibodies made against host cell antigens. These strains are useful producing therapeutic proteins and glycoproteins. The presence of β-mannose structures on N- and/or O-glycans have been demonstrated to elicit an immune response.

Identification of the β-mannosyltransferase genes in Pichia pastoris and Candida albicans was reported in U.S. Pat. No. 7,465,577 and Mille et al., J. Biol. Chem. 283: 9724-9736 (2008), which disclosed that β-mannosylation was effected by a β-mannosyltransferase that was designated AMR2 or BMT2 and that disruption or deletion of the gene in Pichia pastoris resulted a recombinant host that was capable of producing glycoproteins with reduced β-mannosylation. The patent also disclosed three homologues of the gene, BMT1, BMT3, and BMT4. However, when investigating the source of cross binding activity of some glycoprotein preparations to antibodies made against host cell antigens, the inventors discovered that the cross binding activity was a consequence of residual β-mannosylation persisting in some strains of recombinant P. pastoris host cells in which the BMT2 gene had been disrupted or deleted. Thus, heterologous glycoproteins produced in these recombinant host cells have N-glycans that still contained β-mannose residues. These β-mannose residues were detectable in ELISAs and Western blots of the heterologous glycoproteins obtained from cultures of these recombinant host cells probed with antibodies made against host cell antigens (HCA). Anti-HCA antibodies are polyclonal antibodies raised against a wild-type Pichia pastoris strain or a NORF strain: a recombinant host cell that is constructed in the same manner as the recombinant host cell that produces the heterologous glycoprotein except that the open reading frame (ORF) encoding the heterologous protein has been omitted. For therapeutic glycoproteins produced in Pichia pastoris, these residual β-mannose residues present the risk of eliciting an immune response in some individuals that receive the therapeutic protein in a treatment for a disease or disorder. The present invention provides a method for producing glycoproteins in Pichia pastoris that do not contain any detectable β-mannosylation and as such do not cross bind to antibodies made against host cell antigens.

BMT1, BMT2, and BMT3 demonstrate a high degree of sequence homology while BMT4 is homologous to a lower extent and is thought to be a capping alpha-mannosyltransferase. However, all four members of the BMT family appear to be involved in synthesis of N- and/or O-glycans having β-linked mannose structures. Although a MALDI-TOF of N-glycans from a test protein produced in a Pichia pastoris strain in which the BMT2 gene has been deleted might fail to detect β-mannosylation, the sensitive antibody-based assays herein were able to detect β-mannosylation in Δbmt2 strains. Thus, the anti-HCA antibody-based detection methods taught herein showed that deletion or disruption of also the BMT1 and BMT3 genes and optionally the BMT4 gene was needed to remove all detectable β-mannose structures. Deleting or disrupting the genes encoding the three β-mannosyltransferases can be achieved by (1) complete or partial knock-out of the gene (including the promoter sequences, open reading frame (ORF) and/or the transcription terminator sequences); (2) introduction of a frame-shift in the ORF; (3) inactivation or regulation of the promoter; (4) knock-down of message by siRNA or antisense RNA; (5) or the use of chemical inhibitors. The result is the production of a host cell that is capable of producing a glycoprotein that lacks detectable cross binding activity to anti-HCA antibodies.

To exemplify the methods for producing a glycoprotein that lacks detectable cross binding activity to anti-HCA antibodies, a strain of Pichia pastoris, which had been genetically engineered to lack BMT2 expression or activity and to be capable of producing recombinant mature human erythropoietin (EPO) with sialic acid-terminated bi-antennary N-glycans, was further genetically engineered to lack expression of the BMT1 and/or BMT3 and/or BMT4 genes. The strain in which only expression of the BMT2 gene had been disrupted produced recombinant mature human EPO having some detectable cross binding activity to anti-HCA antibodies. The detectable cross binding activity was found to be due to the presence of β-linked mannose residues on the EPO molecule (See FIGS. 22-27B, Example 6). When the genes encoding BMT1 and BMT4 were disrupted or deleted in the strain, the EPO produced still had detectable cross binding activity to anti-HCA antibodies (See FIGS. 28-31). However, when the BMT1, BMT2, BMT3, and BMT4 genes were disrupted or deleted, most of the strains produced glycosylated recombinant human EPO that lacked detectable cross binding activity to anti-HCA antibodies and thus lacked detectable β-mannose residues (See FIGS. 33 and 35B for example).

Thus, the present invention further provides a method for producing a recombinant protein or glycoprotein that lacks detectable cross binding activity to antibodies made against host cell antigens that involves constructing host cells intended to be used to produce the recombinant protein to further not display various combinations β-mannosyltransferase activities. By way of example, a host cell is constructed that does not display β-mannosylttransferase 2 activity with respect to an N-glycan or O-glycan. The host cell lacking display β-mannosyltransferase 2 activity is used to produce the recombinant protein or glycoprotein, which is then evaluated by Western blot or ELISA using an antibody that has been made against a NORF version of the strain. A NORF strain is a strain the same as the host strain except it lacks the open reading frame encoding the recombinant glycoprotein. If the recombinant protein or glycoprotein produced by the host cell lacks detectable binding to the antibody made against host cell antigens, then the host cell is useful for producing the recombinant protein or glycoprotein that lacks cross binding activity to the antibodies against host cell antigens.

However, if detectable cross binding activity is detected, then the host cell is further manipulated to not display β-mannosyltransferase 1, β-mannosyltransferase 3, or β-mannosyltransferase 4 activity with respect to an N-glycan or O-glycan. For example, the host cell that lacks β-mannosyltransferase 2 activity is further manipulated to lack β-mannosyltransferase 1 activity. The host cell is used to produce the recombinant protein or glycoprotein, which is then evaluated by Western blot or ELISA using an antibody that has been made against a NORF version of the strain. If the recombinant protein or glycoprotein produced by the host cell lacks detectable binding to the antibody made against host cell antigens, then the host cell is useful for producing the recombinant protein or glycoprotein that lacks cross binding activity to the antibodies against host cell antigens.

However, if detectable cross binding activity is detected, then the host cell is further manipulated to not display β-mannosyltransferase 3 activity or β-mannosyltransferase 4 activity. For example, the host cell that lacks β-mannosyltransferase 2 activity and β-mannosyltransferase 1 activity is further manipulated to lack β-mannosyltransferase 3 activity with respect to an N-glycan or O-glycan. The host cell is used to produce the protein or recombinant glycoprotein, which is then evaluated by Western blot or ELISA using an antibody that has been made against a NORF version of the strain. If the recombinant protein or glycoprotein produced by the host cell lacks detectable binding to the antibody made against host cell antigens, then the host cell is useful for producing the recombinant protein or glycoprotein that lacks cross binding activity to the antibodies against host cell antigens.

However, if detectable cross binding activity is detected, then the strain is further manipulated to not display β-mannosyltransferase 4 activity with respect to an N-glycan or O-glycan. The host cell is used to produce the recombinant protein or glycoprotein, which is then evaluated by Western blot or ELISA using an antibody that has been made against a NORF version of the strain to confirm that the recombinant protein or glycoprotein lacks detectable binding to the antibody made against host cell antigens.

By way of a further example, a Pichia pastoris host cell is constructed in which various combinations of BMT genes are deleted or disrupted in. By way of example, a Pichia pastoris host cell is constructed that has a disruption or deletion of the BMT2 gene. The Δbmt2 host cell is used to produce the recombinant protein or glycoprotein, which is then evaluated by Western blot or ELISA using an antibody that has been made against a NORF version of the strain. A NORF strain is a strain the same as the host strain except it lacks the open reading frame encoding the recombinant glycoprotein. If the recombinant protein or glycoprotein produced by the Δbmt2 host cell lacks detectable binding to the antibody made against host cell antigens, then the BMT2 deletion or disruption is sufficient to enable the host cell to produce the recombinant protein or glycoprotein that lacks cross binding activity to the antibodies against host cell antigens.

However, if detectable cross binding activity is detected, then the host cell is further manipulated to have a deletion of the BMT1, BMT3, or BMT4 genes. For example, the host cell that has a disruption or deletion of the BMT2 gene is further manipulated to have a deletion or disruption of the BMT1 gene. The Δbmt2 Δbmt1 host cell is used to produce the recombinant protein or glycoprotein, which is then evaluated by Western blot or ELISA using an antibody that has been made against a NORF version of the strain. If the recombinant protein or glycoprotein produced by the Δbmt2 Δbmt1 host cell lacks detectable binding to the antibody made against host cell antigens, then the BMT1 and BMT2 deletions or disruptions are sufficient to enable the host cell to produce the recombinant protein or glycoprotein that lacks cross binding activity to the antibodies against host cell antigens.

However, if detectable cross binding activity is detected, then the host cell is further manipulated to have a deletion of the BMT3 or BMT4 genes. For example, the host cell that has a disruption or deletion of the BMT1 and BMT2 gene is further manipulated to have a deletion or disruption of the BMT3 gene. The Δbmt2 Δbmt1 Δbmt3 host cell is used to produce the protein or recombinant glycoprotein, which is then evaluated by Western blot or ELISA using an antibody that has been made against a NORF version of the host cell. If the recombinant protein or glycoprotein produced by the Δbmt2 Δbmt1 Δbmt3 host cell lacks detectable binding to the antibody made against host cell antigens, then the BMT1, BMT2, and BMT3 deletions or disruptions are sufficient to enable the host cell to produce the recombinant protein or glycoprotein that lacks cross binding activity to the antibodies against host cell antigens.

However, if detectable cross binding activity is detected, then the host cell is further manipulated to have a deletion of the BMT4 gene. The Δbmt2 Δbmt1 Δbmt3 Δbmt4 host cell is used to produce the recombinant protein or glycoprotein, which is then evaluated by Western blot or ELISA using an antibody that has been made against a NORF version of the strain to confirm that the recombinant protein or glycoprotein lacks detectable binding to the antibody made against host cell antigens.

The present invention further provides a recombinant methylotrophic yeast host cells such as Pichia pastoris host cell in which the host cell does not display a β-mannosyltransferase 2 activity with respect to an N-glycan or O-glycan and does not display at least one of a β-mannosyltransferase 1 activity or a β-mannosyltransferase 3 activity with respect to an N-glycan or O-glycan and which includes a nucleic acid molecule encoding the recombinant protein or glycoprotein. In further embodiments, the host cell does not display β-mannosyltransferase 2 activity, β-mannosyltransferase 1 activity, and β-mannosyltransferase 3 activity with respect to an N-glycan or O-glycan. In a further aspect, the present invention provides a recombinant host cell that does not display a β-mannosyltransferase 2 activity, β-mannosyltransferase 1 activity, β-mannosyltransferase 3 activity, and β-mannosyltransferase 4 activity with respect to an N-glycan or O-glycan and which includes a nucleic acid molecule encoding the recombinant protein or glycoprotein.

The present invention further provides a general method for producing a recombinant protein or glycoprotein that lacks detectable cross binding activity to anti-host cell antigen antibodies comprising providing a recombinant methylotrophic yeast such as Pichia pastoris host cell does not display a β-mannosyltransferase 2 activity with respect to an N-glycan or O-glycan and does not display at least one activity selected from β-mannosyltransferase 1 activity and β-mannosyltransferase 3 activity with respect to an N-glycan or O-glycan and which includes a nucleic acid molecule encoding the recombinant protein or glycoprotein; growing the host cell in a medium under conditions effective for expressing the recombinant protein or glycoprotein; and recovering the recombinant protein or glycoprotein from the medium to produce the recombinant protein or glycoprotein that lacks detectable cross binding activity with antibodies made against host cell antigens. In further embodiments, the host cell lacks β-mannosyltransferase 2 activity, β-mannosyltransferase 1 activity, and β-mannosyltransferase 3 activity with respect to an N-glycan or O-glycan.

In a further aspect, the present invention provides a general method for producing a recombinant protein or glycoprotein that lacks detectable cross binding activity to anti-host cell antigen antibodies comprising providing a recombinant methylotrophic yeast such as Pichia pastoris host cell that does not display β-mannosyltransferase 2 activity, β-mannosyltransferase 1 activity, β-mannosyltransferase 3 activity, and β-mannosyltransferase 4 activity with respect to an N-glycan or O-glycan and which includes a nucleic acid molecule encoding the recombinant protein or glycoprotein; growing the host cell in a medium under conditions effective for expressing the recombinant protein or glycoprotein; and recovering the recombinant protein or glycoprotein from the medium to produce the recombinant protein or glycoprotein that lacks detectable cross binding activity with antibodies made against host cell antigens.

The present invention further provides a recombinant methylotrophic yeast host cells such as Pichia pastoris host cell in which the gene encoding a β-mannosyltransferase 2 activity with respect to an N-glycan or O-glycan has been deleted or disrupted and at least one gene encoding a β-mannosyltransferase 1 activity or β-mannosyltransferase 3 activity with respect to an N-glycan or O-glycan has been deleted or disrupted and which includes a nucleic acid molecule encoding the recombinant protein or glycoprotein. In further embodiments, the genes encoding a β-mannosyltransferase 2 activity, a β-mannosyltransferase 1 activity, and a β-mannosyltransferase 3 activity with respect to an N-glycan or O-glycan have been deleted or disrupted. In a further aspect, the present invention provides a recombinant host cell the genes encoding a β-mannosyltransferase 2 activity, a β-mannosyltransferase 1 activity, a β-mannosyltransferase 3 activity, and β-mannosyltransferase 4 activity with respect to an N-glycan or O-glycan have been deleted or disrupted and which includes a nucleic acid molecule encoding the recombinant protein or glycoprotein.

The present invention further provides a general method for producing a recombinant protein or glycoprotein that lacks detectable cross binding activity to anti-host cell antigen antibodies comprising providing a recombinant methylotrophic yeast such as Pichia pastoris host cell in which the gene encoding a β-mannosyltransferase 2 activity with respect to an N-glycan or O-glycan has been deleted or disrupted and at least one gene encoding an activity selected from β-mannosyltransferase 1 activity and β-mannosyltransferase 3 activity with respect to an N-glycan or O-glycan has been deleted or disrupted and which includes a nucleic acid molecule encoding the recombinant protein or glycoprotein; growing the host cell in a medium under conditions effective for expressing the recombinant protein or glycoprotein; and recovering the recombinant protein or glycoprotein from the medium to produce the recombinant protein or glycoprotein that lacks detectable cross binding activity with antibodies made against host cell antigens. In further embodiments, the genes encoding a β-mannosyltransferase 2 activity, a β-mannosyltransferase 1 activity, and a β-mannosyltransferase 3 activity with respect to an N-glycan or O-glycan have been deleted or disrupted.

In a further aspect, the present invention provides a general method for producing a recombinant protein or glycoprotein that lacks detectable cross binding activity to anti-host cell antigen antibodies comprising providing a recombinant methylotrophic yeast such as Pichia pastoris host cell in which the genes encoding a β-mannosyltransferase 2 activity, a β-mannosyltransferase 1 activity, a β-mannosyltransferase 3 activity, and a β-mannosyltransferase 4 activity with respect to an N-glycan or O-glycan have been deleted or disrupted and which includes a nucleic acid molecule encoding the recombinant protein or glycoprotein; growing the host cell in a medium under conditions effective for expressing the recombinant protein or glycoprotein; and recovering the recombinant protein or glycoprotein from the medium to produce the recombinant protein or glycoprotein that lacks detectable cross binding activity with antibodies made against host cell antigens.

The present invention further provides a recombinant Pichia pastoris host cell in which the BMT2 gene and at least one of BMT1 gene and BMT3 gene have been deleted or disrupted and which includes a nucleic acid molecule encoding the recombinant protein or glycoprotein. In further embodiments, the BMT2 gene, BMT1 gene, and BMT3 gene have been deleted or disrupted. In a further aspect, the present invention provides a recombinant Pichia pastoris host cell in which the BMT1 gene, BMT2 gene, BMT3 gene, and BMT4 gene have been deleted or disrupted and which includes a nucleic acid molecule encoding the recombinant protein or glycoprotein.

The present invention further provides a general method for producing a recombinant protein or glycoprotein that lacks detectable cross binding activity to anti-host cell antigen antibodies comprising providing a recombinant Pichia pastoris host cell in which the BMT2 gene and at least one of the BMT1 gene and the BMT3 gene have been deleted or disrupted and which includes a nucleic acid molecule encoding the recombinant protein or glycoprotein; growing the host cell in a medium under conditions effective for expressing the recombinant protein or glycoprotein; and recovering the recombinant protein or glycoprotein from the medium to produce the recombinant protein or glycoprotein that lacks detectable cross binding activity with antibodies made against host cell antigens. In further embodiments, the BMT2 gene, BMT1 gene, and BMT3 gene have been deleted or disrupted.

In a further aspect, the present invention provides a general method for producing a recombinant protein or glycoprotein that lack detectable cross binding activity to anti-host cell antigen antibodies comprising providing a recombinant Pichia pastoris host cell in which the BMT1 gene, BMT2 gene, BMT3 gene, and BMT4 gene have been deleted or disrupted and which includes a nucleic acid molecule encoding the recombinant protein or glycoprotein; growing the host cell in a medium under conditions effective for expressing the recombinant protein or glycoprotein; and recovering the recombinant protein or glycoprotein from the medium to produce the recombinant protein or glycoprotein that lacks detectable cross binding activity with antibodies made against host cell antigens.

The present invention further provides a recombinant Pichia pastoris host cell in which the BMT2 gene and at least one of the BMT1 gene and the BMT3 gene have been deleted or disrupted and which includes a nucleic acid molecule encoding the recombinant protein or glycoprotein. In further embodiments, the BMT2 gene, BMT1 gene, and BMT3 gene have been deleted or disrupted. In a further aspect, the present invention provides a recombinant Pichia pastoris host cell in which the BMT1 gene, BMT2 gene, BMT3 gene, and BMT4 gene have been deleted or disrupted and which includes a nucleic acid molecule encoding the recombinant protein or glycoprotein.

In general, the recombinant protein or glycoprotein is a therapeutic glycoprotein. Examples of therapeutic glycoproteins contemplated, include but are not limited to erythropoietin (EPO); cytokines such as interferon α, interferon β, interferon γ, and interferon ω; and granulocyte-colony stimulating factor (GCSF); GM-CSF; coagulation factors such as factor VIII, factor IX, and human protein C; antithrombin III; thrombin; soluble IgE receptor α-chain; immunoglobulins such as IgG, IgG fragments, IgG fusions, and IgM; immunoadhesions and other Fc fusion proteins such as soluble TNF receptor-Fc fusion proteins; RAGE-Fc fusion proteins; interleukins; urokinase; chymase; and urea trypsin inhibitor; IGF-binding protein; epidermal growth factor; growth hormone-releasing factor; annexin V fusion protein; angiostatin; vascular endothelial growth factor-2; myeloid progenitor inhibitory factor-1; osteoprotegerin; α-1-antitrypsin; α-feto proteins; DNase II; kringle 3 of human plasminogen; glucocerebrosidase; TNF binding protein 1; follicle stimulating hormone; cytotoxic T lymphocyte associated antigen 4—Ig; transmembrane activator and calcium modulator and cyclophilin ligand; glucagon like protein 1; and IL-2 receptor agonist. In particular aspects of the invention, the nucleic acid molecule encoding the recombinant protein or glycoprotein is codon-optimized to enhance expression of the recombinant protein or glycoprotein in the host cell. For example, as shown in the examples, the nucleic acid molecule encoding the human mature form of erythropoietin was codon-optimized for enhanced expression of the erythropoietin in a methylotrophic yeast such as Pichia pastoris strain that had been genetically engineered to produce an erythropoietin variant comprising bi-antennary N-glycans in which the predominant glycoform comprised both antennae terminally sialylated.

The present invention further provides compositions comprising one or more proteins or glycoproteins lacking detectable cross-binding to antibodies against host cell antigens produced using the methods herein and in the host cells described herein. The compositions can further include pharmaceutically acceptable carriers and salts.

Suitable host cells include any host cell that includes homologues of the Pichia pastoris BMT1, BMT2, BMT3, and/or BMT4 genes. Currently, examples of such host cells include Candida albicans and the methylotrophic yeast Pichia pastoris. Thus, in particular aspects of the invention, the host cell is a methylotrophic yeast such as Pichia pastoris and mutants thereof and genetically engineered variants thereof. Methylotrophic yeast such as Pichia pastoris that are contemplated for use in the present invention can be genetically modified so that they express glycoproteins in which the glycosylation pattern is human-like or humanized. In this manner, glycoprotein compositions can be produced in which a specific desired glycoform is predominant in the composition. Such can be achieved by eliminating selected endogenous glycosylation enzymes and/or genetically engineering the host cells and/or supplying exogenous enzymes to mimic all or part of the mammalian glycosylation pathway as described in US 2004/0018590. If desired, additional genetic engineering of the glycosylation can be performed, such that the glycoprotein can be produced with or without core fucosylation. Use of lower eukaryotic host cells is further advantageous in that these cells are able to produce highly homogenous compositions of glycoprotein, such that the predominant glycoform of the glycoprotein may be present as greater than thirty mole percent of the glycoprotein in the composition. In particular aspects, the predominant glycoform may be present in greater than forty mole percent, fifty mole percent, sixty mole percent, seventy mole percent and, most preferably, greater than eighty mole percent of the glycoprotein present in the composition. Such can be achieved by eliminating selected endogenous glycosylation enzymes and/or supplying exogenous enzymes as described by Gerngross et al., U.S. Pat. No. 7,029,872 and U.S. Pat. No. 7,449,308. For example, a host cell can be selected or engineered to be depleted in 1,6-mannosyl transferase activities, which would otherwise add mannose residues onto the N-glycan on a glycoprotein.

In one embodiment, the host cell further includes an α1,2-mannosidase catalytic domain fused to a cellular targeting signal peptide not normally associated with the catalytic domain and selected to target the α1,2-mannosidase activity to the ER or Golgi apparatus of the host cell. Passage of a recombinant glycoprotein through the ER or Golgi apparatus of the host cell produces a recombinant glycoprotein comprising a Man₅GlcNAc₂ glycoform, for example, a recombinant glycoprotein composition comprising predominantly a Man₅GlcNAc₂ glycoform. For example, U.S. Pat. No. 7,029,872, U.S. Pat. No. 7,449,308, and U.S. Published Patent Application No. 2005/0170452 disclose lower eukaryote host cells capable of producing a glycoprotein comprising a Man₅GlcNAc₂ glycoform.

In a further embodiment, the immediately preceding host cell further includes an N-acetylglucosaminyltransferase I (GlcNAc transferase I or GnT I) catalytic domain fused to a cellular targeting signal peptide not normally associated with the catalytic domain and selected to target GlcNAc transferase I activity to the ER or Golgi apparatus of the host cell. Passage of the recombinant glycoprotein through the ER or Golgi apparatus of the host cell produces a recombinant glycoprotein comprising a GlcNAcMan₅GlcNAc₂ glycoform, for example a recombinant glycoprotein composition comprising predominantly a GlcNAcMan₅GlcNAc₂ glycoform. U.S. Pat. No. 7,029,872, U.S. Pat. No. 7,449,308, and U.S. Published Patent Application No. 2005/0170452 disclose lower eukaryote host cells capable of producing a glycoprotein comprising a GlcNAcMan₅GlcNAc₂ glycoform. The glycoprotein produced in the above cells can be treated in vitro with a hexaminidase to produce a recombinant glycoprotein comprising a Man₅GlcNAc₂ glycoform.

In a further embodiment, the immediately preceding host cell further includes a mannosidase II catalytic domain fused to a cellular targeting signal peptide not normally associated with the catalytic domain and selected to target mannosidase II activity to the ER or Golgi apparatus of the host cell. Passage of the recombinant glycoprotein through the ER or Golgi apparatus of the host cell produces a recombinant glycoprotein comprising a GlcNAcMan₃GlcNAc₂ glycoform, for example a recombinant glycoprotein composition comprising predominantly a GlcNAcMan₃GlcNAc₂ glycoform. U.S. Pat. No. 7,029,872 and U.S. Published Patent Application No. 2004/0230042 discloses lower eukaryote host cells that express mannosidase II enzymes and are capable of producing glycoproteins having predominantly a GlcNAc₂Man₃GlcNAc₂ glycoform. The glycoprotein produced in the above cells can be treated in vitro with a hexaminidase to produce a recombinant glycoprotein comprising a Man₃GlcNAc₂ glycoform.

In a further embodiment, the immediately preceding host cell further includes N-acetylglucosaminyltransferase II (GlcNAc transferase II or GnT II) catalytic domain fused to a cellular targeting signal peptide not normally associated with the catalytic domain and selected to target GlcNAc transferase II activity to the ER or Golgi apparatus of the host cell. Passage of the recombinant glycoprotein through the ER or Golgi apparatus of the host cell produces a recombinant glycoprotein comprising a GlcNAc₂Man₃GlcNAc₂ glycoform, for example a recombinant glycoprotein composition comprising predominantly a GlcNAc₂Man₃GlcNAc₂ glycoform. U.S. Pat. No. 7,029,872 and U.S. Published Patent Application Nos. 2004/0018590 and 2005/0170452 disclose lower eukaryote host cells capable of producing a glycoprotein comprising a GlcNAc₂Man₃GlcNAc₂ glycoform. The glycoprotein produced in the above cells can be treated in vitro with a hexaminidase to produce a recombinant glycoprotein comprising a Man₃GlcNAc₂ glycoform.

In a further embodiment, the immediately preceding host cell further includes a galactosyltransferase catalytic domain fused to a cellular targeting signal peptide not normally associated with the catalytic domain and selected to target galactosyltransferase activity to the ER or Golgi apparatus of the host cell. Passage of the recombinant glycoprotein through the ER or Golgi apparatus of the host cell produces a recombinant glycoprotein comprising a GalGlcNAc₂Man₃GlcNAc₂ or Gal₂GlcNAc₂Man₃GlcNAc₂ glycoform, or mixture thereof for example a recombinant glycoprotein composition comprising predominantly a GalGlcNAc₂Man₃GlcNAc₂ glycoform or Gal₂GlcNAc₂Man₃GlcNAc₂ glycoform or mixture thereof U.S. Pat. No. 7,029,872 and U.S. Published Patent Application No. 2006/0040353 discloses lower eukaryote host cells capable of producing a glycoprotein comprising a Gal₂GlcNAc₂Man₃GlcNAc₂ glycoform. The glycoprotein produced in the above cells can be treated in vitro with a galactosidase to produce a recombinant glycoprotein comprising a GlcNAc₂Man₃GlcNAc₂ glycoform, for example a recombinant glycoprotein composition comprising predominantly a GlcNAc₂Man₃GlcNAc₂ glycoform.

In a further embodiment, the immediately preceding host cell further includes a sialyltransferase catalytic domain fused to a cellular targeting signal peptide not normally associated with the catalytic domain and selected to target sialytransferase activity to the ER or Golgi apparatus of the host cell. Passage of the recombinant glycoprotein through the ER or Golgi apparatus of the host cell produces a recombinant glycoprotein comprising predominantly a NANA₂Gal₂GlcNAc₂Man₃GlcNAc₂ glycoform or NANAGal₂GlcNAc₂Man₃GlcNAc₂ glycoform or mixture thereof. For lower eukaryote host cells such as yeast and filamentous fungi, it is useful that the host cell further include a means for providing CMP-sialic acid for transfer to the N-glycan. U.S. Published Patent Application No. 2005/0260729 discloses a method for genetically engineering lower eukaryotes to have a CMP-sialic acid synthesis pathway and U.S. Published Patent Application No. 2006/0286637 discloses a method for genetically engineering lower eukaryotes to produce sialylated glycoproteins. The glycoprotein produced in the above cells can be treated in vitro with a neuraminidase to produce a recombinant glycoprotein comprising predominantly a Gal₂GlcNAc₂Man₃GlcNAc₂ glycoform or GalGlcNAc₂Man₃GlcNAc₂ glycoform or mixture thereof.

Any one of the preceding host cells can further include one or more GlcNAc transferase selected from the group consisting of GnT III, GnT IV, GnT V, GnT VI, and GnT IX to produce glycoproteins having bisected (GnT III) and/or multiantennary (GnT IV, V, VI, and IX) N-glycan structures such as disclosed in U.S. Published Patent Application Nos. 2004/074458 and 2007/0037248.

In further embodiments, the host cell that produces glycoproteins that have predominantly GlcNAcMan₅GlcNAc₂ N-glycans further includes a galactosyltransferase catalytic domain fused to a cellular targeting signal peptide not normally associated with the catalytic domain and selected to target Galactosyltransferase activity to the ER or Golgi apparatus of the host cell. Passage of the recombinant glycoprotein through the ER or Golgi apparatus of the host cell produces a recombinant glycoprotein comprising predominantly the GalGlcNAcMan₅GlcNAc₂ glycoform.

In a further embodiment, the immediately preceding host cell that produced glycoproteins that have predominantly the GalGlcNAcMan₅GlcNAc₂ N-glycans further includes a sialyltransferase catalytic domain fused to a cellular targeting signal peptide not normally associated with the catalytic domain and selected to target sialytransferase activity to the ER or Golgi apparatus of the host cell. Passage of the recombinant glycoprotein through the ER or Golgi apparatus of the host cell produces a recombinant glycoprotein comprising a NANAGalGlcNAcMan₅GlcNAc₂ glycoform.

In further aspects, any one of the aforementioned host cells, the host cell is further modified to include a fucosyltransferase and a pathway for producing fucose and transporting fucose into the ER or Golgi. Examples of methods for modifying Pichia pastoris to render it capable of producing glycoproteins in which one or more of the N-glycans thereon are fucosylated are disclosed in PCT International Application No. PCT/US2008/002787. In particular aspects of the invention, the Pichia pastoris host cell is further modified to include a fucosylation pathway comprising a GDP-mannose-4,6-dehydratase, GDP-keto-deoxy-mannose-epimerase/GDP-keto-deoxy-galactose-reductase, GDP-fucose transporter, and a fucosyltransferase. In particular aspects, the fucosyltransferase is selected from the group consisting of fucosyltransferase is selected from the group consisting of α1,2-fucosyltransferase, α1,3-fucosyltransferase, α1,4-fucosyltransferase, and α1,6-fucosyltransferase.

Various of the preceding host cells further include one or more sugar transporters such as UDP-GlcNAc transporters (for example, Kluyveromyces lactis and Mus musculus UDP-GlcNAc transporters), UDP-galactose transporters (for example, Drosophila melanogaster UDP-galactose transporter), and CMP-sialic acid transporter (for example, human sialic acid transporter). Because lower eukaryote host cells such as yeast and filamentous fungi lack the above transporters, it is preferable that lower eukaryote host cells such as yeast and filamentous fungi be genetically engineered to include the above transporters.

Host cells further include Pichia pastoris that are genetically engineered to eliminate glycoproteins having phosphomannose residues by deleting or disrupting one or both of the phosphomannosyl transferase genes PNO1 and MNN4B (See for example, U.S. Pat. Nos. 7,198,921 and 7,259,007), which in further aspects can also include deleting or disrupting the MNN4A gene. Disruption includes disrupting the open reading frame encoding the particular enzymes or disrupting expression of the open reading frame or abrogating translation of RNAs encoding one or more of the β-mannosyltransferases and/or phosphomannosyltransferases using interfering RNA, antisense RNA, or the like. The host cells can further include any one of the aforementioned host cells modified to produce particular N-glycan structures.

Host cells further include lower eukaryote cells (e.g., yeast such as Pichia pastoris) that are genetically modified to control O-glycosylation of the glycoprotein by deleting or disrupting one or more of the protein O-mannosyltransferase (Dol-P-Man:Protein (Ser/Thr) Mannosyl Transferase genes) (PMTs) (See U.S. Pat. No. 5,714,377) or grown in the presence of Pmtp inhibitors and/or an alpha-mannosidase as disclosed in Published International Application No. WO 2007061631, or both. Disruption includes disrupting the open reading frame encoding the Pmtp or disrupting expression of the open reading frame or abrogating translation of RNAs encoding one or more of the Pmtps using interfering RNA, antisense RNA, or the like. The host cells can further include any one of the aforementioned host cells modified to produce particular N-glycan structures.

Pmtp inhibitors include but are not limited to a benzylidene thiazolidinediones. Examples of benzylidene thiazolidinediones that can be used are 5-[[3,4-bis(phenylmethoxy)phenyl]methylene]-4-oxo-2-thioxo-3-thiazolidineacetic Acid; 5-[[3-(1-Phenylethoxy)-4-(2-phenylethoxy)]phenyl]methylene]-4-oxo-2-thioxo-3-thiazolidineacetic Acid; and 5-[[3-(1-Phenyl-2-hydroxy)ethoxy)-4-(2-phenylethoxy)]phenyl]methylene]-4-oxo-2-thioxo-3-thiazolidineacetic Acid.

In particular embodiments, the function or expression of at least one endogenous PMT gene is reduced, disrupted, or deleted. For example, in particular embodiments the function or expression of at least one endogenous PMT gene selected from the group consisting of the PMT1, PMT2, PMT3, and PMT4 genes is reduced, disrupted, or deleted; or the host cells are cultivated in the presence of one or more PMT inhibitors. In further embodiments, the host cells include one or more PMT gene deletions or disruptions and the host cells are cultivated in the presence of one or more Pmtp inhibitors. In particular aspects of these embodiments, the host cells also express a secreted alpha-1,2-mannosidase.

PMT deletions or disruptions and/or Pmtp inhibitors control O-glycosylation by reducing O-glycosylation occupancy; that is by reducing the total number of O-glycosylation sites on the glycoprotein that are glycosylated. The further addition of an alpha-1,2-mannosidase that is secreted by the cell controls O-glycosylation by reducing the mannose chain length of the O-glycans that are on the glycoprotein. Thus, combining PMT deletions or disruptions and/or Pmtp inhibitors with expression of a secreted alpha-1,2-mannosidase controls O-glycosylation by reducing occupancy and chain length. In particular circumstances, the particular combination of PMT deletions or disruptions, Pmtp inhibitors, and alpha-1,2-mannosidase is determined empirically as particular heterologous glycoproteins (antibodies, for example) may be expressed and transported through the Golgi apparatus with different degrees of efficiency and thus may require a particular combination of PMT deletions or disruptions, Pmtp inhibitors, and alpha-1,2-mannosidase. In another aspect, genes encoding one or more endogenous mannosyltransferase enzymes are deleted. This deletion(s) can be in combination with providing the secreted alpha-1,2-mannosidase and/or PMT inhibitors or can be in lieu of providing the secreted alpha-1,2-mannosidase and/or PMT inhibitors.

Thus, the control of O-glycosylation can be useful for producing particular glycoproteins in the host cells disclosed herein in better total yield or in yield of properly assembled glycoprotein. The reduction or elimination of O-glycosylation appears to have a beneficial effect on the assembly and transport of glycoproteins such as whole antibodies as they traverse the secretory pathway and are transported to the cell surface. Thus, in cells in which O-glycosylation is controlled, the yield of properly assembled glycoproteins such as antibody fragments is increased over the yield obtained in host cells in which O-glycosylation is not controlled.

Yield of glycoprotein can in some situations be improved by overexpressing nucleic acid molecules encoding mammalian or human chaperone proteins or replacing the genes encoding one or more endogenous chaperone proteins with nucleic acid molecules encoding one or more mammalian or human chaperone proteins. In addition, the expression of mammalian or human chaperone proteins in the host cell also appears to control O-glycosylation in the cell. Thus, further included are the host cells herein wherein the function of at least one endogenous gene encoding a chaperone protein has been reduced or eliminated, and a vector encoding at least one mammalian or human homolog of the chaperone protein is expressed in the host cell. Also included are host cells in which the endogenous host cell chaperones and the mammalian or human chaperone proteins are expressed. In further aspects, the lower eukaryotic host cell is a yeast or filamentous fungi host cell. Examples of the use of chaperones of host cells in which human chaperone proteins are introduced to improve the yield and reduce or control O-glycosylation of recombinant proteins has been disclosed in PCT International Application No. PCT/US2009/033507. Like above, further included are lower eukaryotic host cells wherein, in addition to replacing the genes encoding one or more of the endogenous chaperone proteins with nucleic acid molecules encoding one or more mammalian or human chaperone proteins or overexpressing one or more mammalian or human chaperone proteins as described above, the function or expression of at least one endogenous gene encoding a protein O-mannosyltransferase (PMT) protein is reduced, disrupted, or deleted. In particular embodiments, the function of at least one endogenous PMT gene selected from the group consisting of the PMT1, PMT2, PMT3, and PMT4 genes is reduced, disrupted, or deleted.

Therefore, the methods disclose herein can use any host cell that has been genetically modified to produce glycoproteins wherein the predominant N-glycan is selected from the group consisting of complex N-glycans, hybrid N-glycans, and high mannose N-glycans wherein complex N-glycans are selected from the group consisting of Man₃GlcNAc₂, GlcNAC₍₁₋₄₎Man₃GlcNAc₂, Gal₍₁₋₄₎GlcNAc₍₁₋₄₎Man₃GlcNAc₂, and NANA₍₁₋₄₎Gal₍₁₋₄₎Man3GlcNAc₂; hybrid N-glycans are selected from the group consisting of Man₅GlcNAc₂, GlcNAcMan₅GlcNAc₂, GalGlcNAcMan₅GlcNAc₂, and NANAGalGlcNAcMan₅GlcNAc₂; and high mannose N-glycans are selected from the group consisting of Man₆GlcNAc₂, Man₇GlcNAc₂, Man₈GlcNAc₂, and Man₉GlcNAc₂. Examples of N-glycan structures include but are not limited to Man₅GlcNAc₂, GlcNAcMan₅GlcNAc₂, GlcNAcMan₃GlcNAc₂, GlcNAc₂Man₃GlcNAc₂, GlcNAc₃Man₃GlcNAc₂, GlcNAc₄Man₃GlcNAc₂, GalGlcNAc₂Man₃GlcNAc₂, Gal₂GlcNAc₂Man₃GlcNAc₂, Gal₂GlcNAc₃Man₃GlcNAc₂, Gal₂GlcNAc₄Man₃GlcNAc₂, Gal₃GlcNAc₃Man₃GlcNAc₂, Gal₃GlcNAc₄Man₃GlcNAc₂, Gal₄GlcNAc₄Man₃GlcNAc₂, NANAGal₂GlcNAc₂Man₃GlcNAc₂, NANA₂Gal₂GlcNAc₂Man₃GlcNAc₂, NANA₃Gal₃GlcNAc₃Man₃GlcNAc₂, and NANA₄Gal₄GlcNAc₄Man₃ GlcNAc₂.

Yeast selectable markers that can be used to construct the recombinant host cells include drug resistance markers and genetic functions which allow the yeast host cell to synthesize essential cellular nutrients, e.g. amino acids. Drug resistance markers which are commonly used in yeast include chloramphenicol, kanamycin, methotrexate, G418 (geneticin), Zeocin, and the like. Genetic functions which allow the yeast host cell to synthesize essential cellular nutrients are used with available yeast strains having auxotrophic mutations in the corresponding genomic function. Common yeast selectable markers provide genetic functions for synthesizing leucine (LEU2), tryptophan (TRP1 and TRP2), proline (PRO1), uracil (URA3, URA5, URA6), histidine (HIS3), lysine (LYS2), adenine (ADE1 or ADE2), and the like. Other yeast selectable markers include the ARR3 gene from S. cerevisiae, which confers arsenite resistance to yeast cells that are grown in the presence of arsenite (Bobrowicz et al., Yeast, 13:819-828 (1997); Wysocki et al., J. Biol. Chem. 272:30061-30066 (1997)). A number of suitable integration sites include those enumerated in U.S. Pat. No. 7,479,389 and include homologs to loci known for Saccharomyces cerevisiae and other yeast or fungi. Methods for integrating vectors into yeast are well known (See for example, U.S. Pat. No. 7,479,389, U.S. Pat. No. 7,514,253, U.S. Published Application No. 2009012400, and WO2009/085135). Examples of insertion sites include, but are not limited to, Pichia ADE genes; Pichia TRP (including TRP1 through TRP2) genes; Pichia MCA genes; Pichia CYM genes; Pichia PEP genes; Pichia PRB genes; and Pichia LEU genes. The Pichia ADE1 and ARG4 genes have been described in Lin Cereghino et al., Gene 263:159-169 (2001) and U.S. Pat. No. 4,818,700, the HIS3 and TRP1 genes have been described in Cosano et al., Yeast 14:861-867 (1998), HIS4 has been described in GenBank Accession No. X56180.

The present invention further provides a method for producing a mature human erythropoietin in methylotrophic yeast such as Pichia pastoris comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens. The method comprises providing a recombinant Pichia pastoris host cell genetically engineered to produce sialic acid-terminated biantennary N-glycans and in which at least the BMT1, BMT2, and BMT3 genes have been deleted or disrupted and which includes two or more nucleic acid molecules, each encoding a fusion protein comprising a mature human erythropoietin EPO fused to a signal peptide that targets the ER or Golgi apparatus and which is removed when the fusion protein is in the ER or Golgi apparatus; growing the host cell in a medium under conditions effective for expressing and processing the first and second fusion proteins; and recovering the mature human erythropoietin from the medium to produce the mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens.

In particular aspects, the nucleic acid molecule encoding the mature human erythropoietin is codon-optimized for optimal expression in the methylotrophic yeast such as Pichia pastoris. As shown in the examples, the mature human erythropoietin is encoded as a fusion protein in which the EPO is fused at the N-terminus of the mature form of the erythropoietin to the C-terminus of a signal peptide that targets the fusion protein to the secretory pathway for processing, including glycosylation. Examples of signal peptides include but are not limited to the S. cerevisiae αMATpre signal peptide or a chicken lysozyme signal peptide. Other signal sequences can be used instead of those disclosed herein, for example, the Aspergillus niger α-amylase signal peptide and human serum albumin (HSA) signal peptide. In one embodiment, a first nucleic acid molecule encodes a fusion protein wherein the mature erythropoietin is fused to the S. cerevisiae αMATpre signal peptide and second nucleic acid molecule encodes a fusion protein wherein the mature erythropoietin is fused to the S. cerevisiae αMATpre signal peptide a chicken lysozyme signal peptide. The signal peptide can be fused to the mature human erythropoietin by a linker peptide that can contain one or more protease cleavage sites.

In further aspects, the host cell includes between two and twelve copies of the expression cassettes encoding the fusion protein comprising the mature human erythropoietin. In some aspects, the host cell includes about eight to eleven copies of the expression cassettes encoding the fusion protein comprising the mature human erythropoietin. In other aspects, the host cell includes about three to four copies of the first nucleic acid and five to seven copies of the second nucleic acid.

The host cell is genetically engineered to produce sialic acid-terminated biantennary N-glycans and in which at least the BMT1, BMT2, and BMT3 genes have been deleted or disrupted. Such a host cell further includes at least a deletion or disruption of the OCH1, PNO1, MNN4, and MNN4L1 genes. The host cell further includes one or more nucleic acid molecules encoding at least the following chimeric glycosylation enzymes: α1,2-mannosidase catalytic domain fused to a cellular targeting peptide that targets the catalytic domain to the ER or Golgi apparatus of the host cell; GlcNAc transferase I catalytic domain fused to a cellular targeting peptide that targets the catalytic domain to the ER or Golgi apparatus of the host cell; mannosidase II catalytic domain fused to a cellular targeting peptide that targets the catalytic domain to the ER or Golgi apparatus of the host cell; GlcNAc transferase II catalytic domain fused to a cellular targeting peptide that targets the catalytic domain to the ER or Golgi apparatus of the host cell; β1,4-galactosyltransferase catalytic domain fused to a cellular targeting peptide that targets the catalytic domain to the ER or Golgi apparatus of the host cell; and α1,2-sialyltransferase catalytic domain fused to a cellular targeting peptide that targets the catalytic domain to the ER or Golgi apparatus of the host cell. These glycosylation enzymes are selected to be active at the location in the ER or Golgi apparatus to which they are targeted. Methods for selecting glycosylation enzymes and targeting the enzymes to particular regions of the ER or Golgi apparatus for optimal activity have been described in U.S. Pat. Nos. 7,029,872 and 7,449,308 and in Published U.S. Application Nos. 2006/0040353 and 2006/0286637. The host cells are further modified to include the enzymes of a pathway as disclosed in Published U.S. Application No. and 2006/0286637 to produce CMP-sialic acid and to include GlcNAc and galactose transporters and a UDP-galactose-4-epimerase. Finally, the host further includes a nucleic acid molecule encoding a fungal α1,2-mannosidase catalytic domain fused to a cellular targeting peptide that targets the catalytic domain to the secretory pathway for secretion and which effects a reduction in O-glycan occupancy and chain length.

Detection of detectable cross binding activity with antibodies made against host cell antigens can be determined in a sandwich ELISA or in a Western blot.

In further aspects, recovering the mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens includes a cation exchange chromatography step and/or a hydroxyapatite chromatography step and/or an anion exchange chromatography step. In one embodiment, the recovering the mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens comprises a cation exchange chromatography step followed by a hydroxyapatite chromatography step. Optionally, recovery of the mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens includes an anion chromatography step.

Further provided is a composition comprising a mature human erythropoietin comprising predominantly sialic acid-terminated bi-antennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens obtained as disclosed herein and a pharmaceutically acceptable salt. In particular embodiments, about 50 to 60% of the N-glycans comprise sialic acid residues on both antennae; in further embodiments, greater than 70% of the N-glycans comprise sialic acid residues on both antennae. In further aspects, less than 30% of the N-glycans are neutral N-glycans (i.e., are not sialylated on at least one terminus at the non-reducing end of the N-glycan). In further still aspects, less than 20% of the N-glycans are neutral N-glycans.

In particular aspects, the mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens is conjugated to a hydrophilic polymer, which is particular embodiments is a polyethylene glycol polymer. Examples of mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans conjugated to polyethylene glycol polymers has been described in commonly-owned U.S. Published Application No. 2008/0139470.

The polyethylene glycol polymer (PEG) group may be of any convenient molecular weight and may be linear or branched. The average molecular weight of the PEG will preferably range from about 2 kiloDalton (“kDa”) to about 100 kDa, more preferably from about 5 kDa to about 60 kDa, more preferably from about 20 kDa to about 50 kDa; most preferably from about 30 kDa to about 40 kDa. These PEGs can be supplied from any commercial vendors including NOF Corporation (Tokyo, Japan), Dow Pharma (ChiroTech Technology, Cambridge, UK), Nektar (San Carlos, Calif.) and SunBio (Anyang City, South Korea). Suitable PEG moieties include, for example, 40 kDa methoxy poly(ethylene glycol) propionaldehyde; 60 kDa methoxy poly(ethylene glycol) propionaldehyde; 31 kDa alpha-methyl-w-β-oxopropoxy), polyoxyethylene; 30 kDa PEG: 30 kDa Methoxy poly(ethylene glycol) propionaldehyde and 45 kDa 2,3-Bis(methylpolyoxyethylene-oxy)-1-[(3-oxopropyl)polyoxyethylene-oxy]-propane. The PEG groups will generally be attached to the erythropoietin via acylation or reductive amination through a reactive group on the PEG moiety (e.g., an aldehyde, amino, thiol, or ester group) to a reactive group on the protein or polypeptide of interest (e.g., an aldehyde, amino, or ester group). For example, the PEG moiety may be linked to the N-terminal amino acid residue of erythropoietin, either directly or through a linker.

A useful strategy for the PEGylation of synthetic peptides consists of combining, through forming a conjugate linkage in solution, a peptide and a PEG moiety, each bearing a special functionality that is mutually reactive toward the other. The peptides can be easily prepared with conventional solid phase synthesis (See, for example, Example 4). The peptides are “preactivated” with an appropriate functional group at a specific site. The precursors are purified and fully characterized prior to reacting with the PEG moiety. Ligation of the peptide with PEG usually takes place in aqueous phase and can be easily monitored by reverse phase analytical HPLC. The PEGylated peptides can be easily purified by preparative HPLC and characterized by analytical HPLC, amino acid analysis and laser desorption mass spectrometry.

The following examples are intended to promote a further understanding of the present invention.

Example 1

Genetically engineered Pichia pastoris strain YGLY3159 is a strain that produces recombinant human erythropoietin with sialylated N-glycans (rhEPO). Construction of the strain has been described in U.S. Published Application No. 20080139470 and is illustrated schematically in FIG. 1. Briefly, the strain was constructed as follows.

The strain YGLY3159 was constructed from wild-type Pichia pastoris strain NRRL-Y 11430 using methods described earlier (See for example, U.S. Pat. No. 7,449,308; U.S. Pat. No. 7,479,389; U.S. Published Application No. 20090124000; Published PCT Application No. WO2009085135; Nett and Gerngross, Yeast 20:1279 (2003); Choi et al., Proc. Natl. Acad. Sci. USA 100:5022 (2003); Hamilton et al., Science 301:1244 (2003)). All plasmids were made in a pUC19 plasmid using standard molecular biology procedures. For nucleotide sequences that were optimized for expression in P. pastoris, the native nucleotide sequences were analyzed by the GENEOPTIMIZER software (GeneArt, Regensburg, Germany) and the results used to generate nucleotide sequences in which the codons were optimized for P. pastoris expression. Yeast strains were transformed by electroporation (using standard techniques as recommended by the manufacturer of the electroporator BioRad).

Plasmid pGLY6 (FIG. 2) is an integration vector that targets the URA5 locus contains a nucleic acid molecule comprising the S. cerevisiae invertase gene or transcription unit (ScSUC2; SEQ ID NO:1) flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region of the P. pastoris URA5 gene (SEQ ID NO:59) and on the other side by a nucleic acid molecule comprising the a nucleotide sequence from the 3′ region of the P. pastoris URA5 gene (SEQ ID NO:60). Plasmid pGLY6 was linearized and the linearized plasmid transformed into wild-type strain NRRL-Y 11430 to produce a number of strains in which the ScSUC2 gene was inserted into the URA5 locus by double-crossover homologous recombination. Strain YGLY1-3 was selected from the strains produced and is auxotrophic for uracil.

Plasmid pGLY40 (FIG. 3) is an integration vector that targets the OCH1 locus and contains a nucleic acid molecule comprising the P. pastoris URA5 gene or transcription unit (SEQ ID NO:61) flanked by nucleic acid molecules comprising lacZ repeats (SEQ ID NO:62) which in turn is flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region of the OCH1 gene (SEQ ID NO:64) and on the other side by a nucleic acid molecule comprising a nucleotide sequence from the 3′ region of the OCH1 gene (SEQ ID NO:65). Plasmid pGLY40 was linearized with SfiI and the linearized plasmid transformed into strain YGLY1-3 to produce to produce a number of strains in which the URA5 gene flanked by the lacZ repeats has been inserted into the OCH1 locus by double-crossover homologous recombination. Strain YGLY2-3 was selected from the strains produced and is prototrophic for URA5. Strain YGLY2-3 was counterselected in the presence of 5-fluoroorotic acid (5-FOA) to produce a number of strains in which the URA5 gene has been lost and only the lacZ repeats remain in the OCH1 locus. This renders the strain auxotrophic for uracil. Strain YGLY4-3 was selected.

Plasmid pGLY43a (FIG. 4) is an integration vector that targets the BMT2 locus and contains a nucleic acid molecule comprising the K. lactis UDP-N-acetylglucosamine (UDP-GlcNAc) transporter gene or transcription unit (KlMNN2-2, SEQ ID NO:3) adjacent to a nucleic acid molecule comprising the P. pastoris URA5 gene or transcription unit flanked by nucleic acid molecules comprising lacZ repeats. The adjacent genes are flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region of the BMT2 gene (SEQ ID NO: 66) and on the other side by a nucleic acid molecule comprising a nucleotide sequence from the 3′ region of the BMT2 gene (SEQ ID NO:67). Plasmid pGLY43a was linearized with SfiI and the linearized plasmid transformed into strain YGLY4-3 to produce to produce a number of strains in which the KlMNN2-2 gene and URA5 gene flanked by the lacZ repeats has been inserted into the BMT2 locus by double-crossover homologous recombination. The BMT2 gene has been disclosed in Mille et al., J. Biol. Chem. 283: 9724-9736 (2008) and U.S. Pat. No. 7,465,557. Strain YGLY6-3 was selected from the strains produced and is prototrophic for uracil. Strain YGLY6-3 was counterselected in the presence of 5-FOA to produce strains in which the URA5 gene has been lost and only the lacZ repeats remain. This renders the strain auxotrophic for uracil. Strain YGLY8-3 was selected.

Plasmid pGLY48 (FIG. 5) is an integration vector that targets the MNN4L1 locus and contains an expression cassette comprising a nucleic acid molecule encoding the mouse homologue of the UDP-GlcNAc transporter (SEQ ID NO:17) open reading frame (ORF) operably linked at the 5′ end to a nucleic acid molecule comprising the P. pastoris GAPDH promoter (SEQ ID NO:53) and at the 3′ end to a nucleic acid molecule comprising the S. cerevisiae CYC termination sequences (SEQ ID NO:56) adjacent to a nucleic acid molecule comprising the P. pastoris URA5 gene flanked by lacZ repeats and in which the expression cassettes together are flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region of the P. Pastoris MNN4L1 gene (SEQ ID NO:76) and on the other side by a nucleic acid molecule comprising a nucleotide sequence from the 3′ region of the MNN4L1 gene (SEQ ID NO:77). Plasmid pGLY48 was linearized with SfiI and the linearized plasmid transformed into strain YGLY8-3 to produce a number of strains in which the expression cassette encoding the mouse UDP-GlcNAc transporter and the URA5 gene have been inserted into the MNN4L1 locus by double-crossover homologous recombination. The MNN4L1 gene (also referred to as MNN4B) has been disclosed in U.S. Pat. No. 7,259,007. Strain YGLY10-3 was selected from the strains produced and then counterselected in the presence of 5-FOA to produce a number of strains in which the URA5 gene has been lost and only the lacZ repeats remain. Strain YGLY12-3 was selected.

Plasmid pGLY45 (FIG. 6) is an integration vector that targets the PNO1/MNN4 loci contains a nucleic acid molecule comprising the P. pastoris URA5 gene or transcription unit flanked by nucleic acid molecules comprising lacZ repeats which in turn is flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region of the PNO1 gene (SEQ ID NO:74) and on the other side by a nucleic acid molecule comprising a nucleotide sequence from the 3′ region of the MNN4 gene (SEQ ID NO:75). Plasmid pGLY45 was linearized with SfiI and the linearized plasmid transformed into strain YGLY12-3 to produce to produce a number of strains in which the URA5 gene flanked by the lacZ repeats has been inserted into the MNN4 loci by double-crossover homologous recombination. The PNO1 gene has been disclosed in U.S. Pat. No. 7,198,921 and the MNN4 gene (also referred to as MNN4B) has been disclosed in U.S. Pat. No. 7,259,007. Strain YGLY14-3 was selected from the strains produced and then counterselected in the presence of 5-FOA to produce a number of strains in which the URA5 gene has been lost and only the lacZ repeats remain. Strain YGLY16-3 was selected.

Plasmid pGLY247 (FIG. 7) is an integration vector that targets the MET16 locus and contains a nucleic acid molecule comprising the P. pastoris URA5 gene or transcription unit flanked by nucleic acid molecules comprising lacZ repeats which in turn is flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region of the MET16 gene (SEQ ID NO:84) and on the other side by a nucleic acid molecule comprising a nucleotide sequence from the 3′ region of the MET16 gene (SEQ ID NO:85). Plasmid pGLY247 was linearized with SfiI and the linearized plasmid transformed into strain YGLY16-3 to produce a number of strains in which the URA5 flanked by the lacZ repeats has been inserted into the MET16 locus by double-crossover homologous recombination. Strain YGLY20-3 was selected.

Plasmid pGLY248 (FIG. 8) is an integration vector that targets the URA5 locus and contains a nucleic acid molecule comprising the P. pastoris MET16 gene (SEQ ID NO:86) flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region of the URA5 gene (SEQ ID NO:59) and on the other side by a nucleic acid molecule comprising a nucleotide sequence from the 3′ region of the URA5 gene (SEQ ID NO:60). Plasmid pGLY248 was linearized and the linearized plasmid transformed into strain YGLY20-3 to produce a number of strains in which the ScSUC2 gene inserted into the URA5 locus has been replaced with the MET16 gene by double-crossover homologous recombination. Strain YGLY22-3 was selected and then counterselected in the presence of 5-FOA to produce a number of strains in which the URA5 gene inserted into the MET16 locus has been lost and only the lacZ repeats remain. Strain YGLY24-3 was selected.

Plasmid pGLY582 (FIG. 9) is an integration vector that targets the HIS1 locus and contains in tandem four expression cassettes encoding (1) the S. cerevisiae UDP-glucose epimerase (ScGAL10), (2) the human galactosyltransferase I (hGalT) catalytic domain fused at the N-terminus to the S. cerevisiae KRE2-s leader peptide (33) to target the chimeric enzyme to the ER or Golgi, (3) the P. pastoris URA5 gene or transcription unit flanked by lacZ repeats, and (4) the D. melanogaster UDP-galactose transporter (DmUGT). The expression cassette encoding the ScGAL10 comprises a nucleic acid molecule encoding the ScGAL10 ORF (SEQ ID NO:21) operably linked at the 5′ end to a nucleic acid molecule comprising the P. pastoris PMA1 promoter (SEQ ID NO:45) and operably linked at the 3′ end to a nucleic acid molecule comprising the P. pastoris PMA1 transcription termination sequence (SEQ ID NO:46). The expression cassette encoding the chimeric galactosyltransferase I comprises a nucleic acid molecule encoding the hGalT catalytic domain codon optimized for expression in P. pastoris (SEQ ID NO:23) fused at the 5′ end to a nucleic acid molecule encoding the KRE2-s leader 33 (SEQ ID NO:13), which is operably linked at the 5′ end to a nucleic acid molecule comprising the P. pastoris GAPDH promoter and at the 3′ end to a nucleic acid molecule comprising the S. cerevisiae CYC transcription termination sequence. The URA5 expression cassette comprises a nucleic acid molecule comprising the P. pastoris URA5 gene or transcription unit flanked by nucleic acid molecules comprising lacZ repeats. The expression cassette encoding the DmUGT comprises a nucleic acid molecule encoding the DmUGT ORF (SEQ ID NO:19) operably linked at the 5′ end to a nucleic acid molecule comprising the P. pastoris OCH1 promoter (SEQ ID NO:47) and operably linked at the 3′ end to a nucleic acid molecule comprising the P. pastoris ALG12 transcription termination sequence (SEQ ID NO:48). The four tandem cassettes are flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region of the HIS1 gene (SEQ ID NO:87) and on the other side by a nucleic acid molecule comprising a nucleotide sequence from the 3′ region of the HIS1 gene (SEQ ID NO:88). Plasmid pGLY582 was linearized and the linearized plasmid transformed into strain YGLY24-3 to produce a number of strains in which the four tandem expression cassette have been inserted into the HIS1 locus by homologous recombination. Strain YGLY58 was selected and is auxotrophic for histidine and prototrophic for uridine.

Plasmid pGLY167b (FIG. 10) is an integration vector that targets the ARG1 locus and contains in tandem three expression cassettes encoding (1) the D. melanogaster mannosidase II catalytic domain (KD) fused at the N-terminus to S. cerevisiae MNN2 leader peptide (53) to target the chimeric enzyme to the ER or Golgi, (2) the P. pastoris HIS1 gene or transcription unit, and (3) the rat N-acetylglucosamine (GlcNAc) transferase II catalytic domain (TC) fused at the N-terminus to S. cerevisiae MNN2 leader peptide (54) to target the chimeric enzyme to the ER or Golgi. The expression cassette encoding the KD53 comprises a nucleic acid molecule encoding the D. melanogaster mannosidase II catalytic domain codon-optimized for expression in P. pastoris (SEQ ID NO:33) fused at the 5′ end to a nucleic acid molecule encoding the MNN2 leader 53 (SEQ ID NO:5), which is operably linked at the 5′ end to a nucleic acid molecule comprising the P. pastoris GAPDH promoter and at the 3′ end to a nucleic acid molecule comprising the S. cerevisiae CYC transcription termination sequence. The HIS1 expression cassette comprises a nucleic acid molecule comprising the P. pastoris HIS1 gene or transcription unit (SEQ ID NO:89). The expression cassette encoding the TC54 comprises a nucleic acid molecule encoding the rat GlcNAc transferase II catalytic domain codon-optimized for expression in P. pastoris (SEQ ID NO:31) fused at the 5′ end to a nucleic acid molecule encoding the MNN2 leader 54 (SEQ ID NO:7), which is operably linked at the 5′ end to a nucleic acid molecule comprising the P. pastoris PMA1 promoter and at the 3′ end to a nucleic acid molecule comprising the P. pastoris PMA1 transcription termination sequence. The three tandem cassettes are flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region of the ARG1 gene (SEQ ID NO:79) and on the other side by a nucleic acid molecule comprising a nucleotide sequence from the 3′ region of the ARG1 gene (SEQ ID NO:80). Plasmid pGLY167b was linearized with SfiI and the linearized plasmid transformed into strain YGLY58 to produce a number of strains (in which the three tandem expression cassette have been inserted into the ARG1 locus by double-crossover homologous recombination. The strain YGLY73 was selected from the strains produced and is auxotrophic for arginine and prototrophic for uridine and histidine. The strain was then counterselected in the presence of 5-FOA to produce a number of strains now auxotrophic for uridine. Strain YGLY1272 was selected.

Plasmid pGLY1430 (FIG. 11) is a KINKO integration vector that targets the ADE1 locus without disrupting expression of the locus and contains in tandem four expression cassettes encoding (1) the human GlcNAc transferase I catalytic domain (NA) fused at the N-terminus to P. pastoris SEC12 leader peptide (10) to target the chimeric enzyme to the ER or Golgi, (2) mouse homologue of the UDP-GlcNAc transporter (MmTr), (3) the mouse mannosidase IA catalytic domain (FB) fused at the N-terminus to S. cerevisiae SEC12 leader peptide (8) to target the chimeric enzyme to the ER or Golgi, and (4) the P. pastoris URA5 gene or transcription unit. KINKO (Knock-In with little or No Knock-Out) integration vectors enable insertion of heterologous DNA into a targeted locus without disrupting expression of the gene at the targeted locus and have been described in U.S. Published Application No. 20090124000. The expression cassette encoding the NA10 comprises a nucleic acid molecule encoding the human GlcNAc transferase I catalytic domain codon-optimized for expression in P. pastoris (SEQ ID NO:25) fused at the 5′ end to a nucleic acid molecule encoding the SEC12 leader 10 (SEQ ID NO:11), which is operably linked at the 5′ end to a nucleic acid molecule comprising the P. pastoris PMA1 promoter and at the 3′ end to a nucleic acid molecule comprising the P. pastoris PMA1 transcription termination sequence. The expression cassette encoding MmTr comprises a nucleic acid molecule encoding the mouse homologue of the UDP-GlcNAc transporter ORF operably linked at the 5′ end to a nucleic acid molecule comprising the P. pastoris SEC4 promoter (SEQ ID NO:49) and at the 3′ end to a nucleic acid molecule comprising the P. pastoris OCH1 termination sequences (SEQ ID NO:50). The expression cassette encoding the FB8 comprises a nucleic acid molecule encoding the mouse mannosidase IA catalytic domain (SEQ ID NO:27) fused at the 5′ end to a nucleic acid molecule encoding the SEC12-m leader 8 (SEQ ID NO:15), which is operably linked at the 5′ end to a nucleic acid molecule comprising the P. pastoris GADPH promoter and at the 3′ end to a nucleic acid molecule comprising the S. cerevisiae CYC transcription termination sequence. The URA5 expression cassette comprises a nucleic acid molecule comprising the P. pastoris URA5 gene or transcription unit flanked by nucleic acid molecules comprising lacZ repeats. The four tandem cassettes are flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region and complete ORF of the ADE1 gene (SEQ ID NO:82) followed by a P. pastoris ALG3 termination sequence (SEQ ID NO:54) and on the other side by a nucleic acid molecule comprising a nucleotide sequence from the 3′ region of the ADE1 gene (SEQ ID NO:83). Plasmid pGLY1430 was linearized with SfiI and the linearized plasmid transformed into strain YGLY1272 to produce a number of strains in which the four tandem expression cassette have been inserted into the ADE1 locus immediately following the ADE1 ORF by double-crossover homologous recombination. The strain YGLY1305 was selected from the strains produced and is auxotrophic for arginine and now prototrophic for uridine, histidine, and adenine. The strain was then counterselected in the presence of 5-FOA to produce a number of strains now auxotrophic for uridine. Strain YGLY1461 was selected and is capable of making glycoproteins that have predominantly galactose terminated N-glcyans.

Plasmid pGFI165 (FIG. 12) is a KINKO integration vector that targets the PRO1 locus without disrupting expression of the locus and contains expression cassettes encoding (1) the T. reesei α-1,2-mannosidase catalytic domain fused at the N-terminus to S. cerevisiae αMATpre signal peptide (aMATTrMan) to target the chimeric protein to the secretory pathway and secretion from the cell and (2) the P. pastoris URA5 gene or transcription unit. The expression cassette encoding the aMATTrMan comprises a nucleic acid molecule encoding the T. reesei catalytic domain (SEQ ID NO:29) fused at the 5′ end to a nucleic acid molecule encoding the S. cerevisiae αMATpre signal peptide (SEQ ID NO:9), which is operably linked at the 5′ end to a nucleic acid molecule comprising the P. pastoris GAPDH promoter and at the 3′ end to a nucleic acid molecule comprising the S. cerevisiae CYC transcription termination sequence. The URA5 expression cassette comprises a nucleic acid molecule comprising the P. pastoris URA5 gene or transcription unit flanked by nucleic acid molecules comprising lacZ repeats. The two tandem cassettes are flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region and complete ORF of the PRO1 gene (SEQ ID NO:90) followed by a P. pastoris ALG3 termination sequence and on the other side by a nucleic acid molecule comprising a nucleotide sequence from the 3′ region of the PRO1 gene (SEQ ID NO:91). Plasmid pGFI165 was linearized with SfiI and the linearized plasmid transformed into strain YGLY1461 to produce a number of strains in which the two expression cassette have been inserted into the PRO1 locus immediately following the PRO1 ORF by double-crossover homologous recombination. The strain YGLY1703 was selected from the strains produced and is auxotrophic for arginine and prototrophic for uridine, histidine, adenine, and proline. This strain is capable of producing glycoproteins that have reduced O-glycosylation (See Published U.S. Application No. 20090170159).

Plasmid pGLY2088 (FIG. 13) is an integration vector that targets the TRP2 or AOX1 locus and contains expression cassettes encoding (1) mature human erythropoetin (EPO) fused at the N-terminus to a S. cerevisiae αMATpre signal peptide (alpha MF-pre) to target the chimeric protein to the secretory pathway and secretion from the cell and (2) the zeocin resistance protein (Sh ble or Zeocin^(R)). The expression cassette encoding the EPO comprises a nucleic acid molecule encoding the mature human EPO codon-optimized for expression in P. pastoris (SEQ ID NO:92) fused at the 5′ end to a nucleic acid molecule encoding the S. cerevisiae αMATpre signal peptide, which is operably linked at the 5′ end to a nucleic acid molecule comprising the P. pastoris AOX1 promoter (SEQ ID NO:55) and at the 3′ end to a nucleic acid molecule comprising the S. cerevisiae CYC transcription termination sequence. The Zeocin^(R) expression cassette comprises a nucleic acid molecule encoding the Sh ble ORF (SEQ ID NO:58) operably linked at the 5′ end to the S. cerevisiae TEF1 promoter (SEQ ID NO:57) and at the 3′ end to the S. cerevisiae CYC termination sequence. The two tandem cassettes are flanked on one side by a nucleic acid molecule comprising a nucleotide sequence comprising the TRP2 gene (SEQ ID NO:78). Plasmid pGLY2088 was linearized at the PmeI site and transformed into strain YGLY1703 to produce a number of strains in which the two expression cassette have been inserted into the AOX1 locus by roll in single-crossover homologous recombination, which results in multiple copies of the EPO expression cassette inserted into the AOX1 locus without disrupting the AOX1 locus. The strain YGLY2849 was selected from the strains produced and is auxotrophic for arginine and now prototrophic for uridine, histidine, adenine, and proline. The strain contains about three to four copies of the EPO expression cassette as determined by measuring the intensity of sequencing data of DNA isolated from the strain. During processing of the chimeric EPO in the ER and Golgi, the leader peptide is removed. Thus, the rhEPO produced is the mature form of the EPO. Plasmid pGLY2456 (FIG. 14) is a KINKO integration vector that targets the TRP2 locus without disrupting expression of the locus and contains six expression cassettes encoding (1) the mouse CMP-sialic acid transporter (mCMP-Sia Transp), (2) the human UDP-GlcNAc 2-epimerase/N-acetylmannosamine kinase (hGNE), (3) the Pichia pastoris ARG1 gene or transcription unit, (4) the human CMP-sialic acid synthase (hCMP-NANA), (5) the human N-acetylneuraminate-9-phosphate synthase (hSIAP S), (6) the mouse a-2,6-sialyltransferase catalytic domain (mST6) fused at the N-terminus to S. cerevisiae KRE2 leader peptide (33) to target the chimeric enzyme to the ER or Golgi, and the P. pastoris ARG1 gene or transcription unit. The expression cassette encoding the mouse CMP-sialic acid Transporter comprises a nucleic acid molecule encoding the mCMP Sia Transp ORF codon optimized for expression in P. pastoris (SEQ ID NO:35), which is operably linked at the 5′ end to a nucleic acid molecule comprising the P. pastoris PMA1 promoter and at the 3′ end to a nucleic acid molecule comprising the P. pastoris PMA1 transcription termination sequence. The expression cassette encoding the human UDP-GlcNAc 2-epimerase/N-acetylmannosamine kinase comprises a nucleic acid molecule encoding the hGNE ORF codon optimized for expression in P. pastoris (SEQ ID NO:37), which is operably linked at the 5′ end to a nucleic acid molecule comprising the P. pastoris GAPDH promoter and at the 3′ end to a nucleic acid molecule comprising the S. cerevisiae CYC transcription termination sequence. The expression cassette encoding the P. pastoris ARG1 gene comprises (SEQ ID NO:81). The expression cassette encoding the human CMP-sialic acid synthase comprises a nucleic acid molecule encoding the hCMP-NANA S ORF codon optimized for expression in P. pastoris (SEQ ID NO:39), which is operably linked at the 5′ end to a nucleic acid molecule comprising the P. pastoris GPDAH promoter and at the 3′ end to a nucleic acid molecule comprising the S. cerevisiae CYC transcription termination sequence. The expression cassette encoding the human N-acetylneuraminate-9-phosphate synthase comprises a nucleic acid molecule encoding the hSIAP S ORF codon optimized for expression in P. pastoris (SEQ ID NO:41), which is operably linked at the 5′ end to a nucleic acid molecule comprising the P. pastoris PMA1 promoter and at the 3′ end to a nucleic acid molecule comprising the P. pastoris PMA1 transcription termination sequence. The expression cassette encoding the chimeric mouse a-2,6-sialyltransferase comprises a nucleic acid molecule encoding the mST6 catalytic domain codon optimized for expression in P. pastoris (SEQ ID NO:43) fused at the 5′ end to a nucleic acid molecule encoding the S. cerevisiae KRE2 signal peptide, which is operably linked at the 5′ end to a nucleic acid molecule comprising the P. pastoris TEF promoter (SEQ ID NO:51) and at the 3′ end to a nucleic acid molecule comprising the P. pastoris TEF transcription termination sequence (SEQ ID NO:52). The six tandem cassettes are flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region of the ORF encoding Trp2p ending at the stop codon (SEQ ID NO:98) followed by a P. pastoris ALG3 termination sequence and on the other side by a nucleic acid molecule comprising a nucleotide sequence from the 3′ region of the TRP2 gene (SEQ ID NO:99). Plasmid pGLY2456 was linearized with SfiI and the linearized plasmid transformed into strain YGLY2849 to produce a number of strains in which the six expression cassette have been inserted into the TRP2 locus immediately following the TRP2 ORF by double-crossover homologous recombination. The strain YGLY3159 was selected from the strains produced and is now prototrophic for uridine, histidine, adenine, proline, arginine, and tryptophan. The strain is resistant to Zeocin and contains about three to four copies of the EPO expression cassette. The strain produced rhEPO; however, using the methods in Example 5, the rhEPO has cross-reactivity binding to antibodies made against HCA (See Example 6).

While the various expression cassettes were integrated into particular loci of the Pichia pastoris genome in the examples herein, it is understood that the operation of the invention is independent of the loci used for integration. Loci other than those disclosed herein can be used for integration of the expression cassettes. Suitable integration sites include those enumerated in U.S. Published Application No. 20070072262 and include homologs to loci known for Saccharomyces cerevisiae and other yeast or fungi.

Example 2

Strain YGLY3159 in Example 1 was further genetically engineered to disrupt the BMT1, BMT3, and BMT4 genes as follows.

Strain YGLY3159 was counterselected in the presence of 5-FOA to produce strain YGLY3225, which is now auxotrophic for uridine.

Plasmid pGLY3411 (pSH1092) (FIG. 15) is an integration vector that contains the expression cassette comprising the P. pastoris URA5 gene flanked by lacZ repeats flanked on one side with the 5′ nucleotide sequence of the P. pastoris BMT4 gene (SEQ ID NO:72) and on the other side with the 3′ nucleotide sequence of the P. pastoris BMT4 gene (SEQ ID NO:73). Plasmid pGLY3411 was linearized and the linearized plasmid transformed into YGLY3159 to produce a number of strains in which the URA5 expression cassette has been inserted into the BMT4 locus by double-crossover homologous recombination. Strain YGLY4439 was selected from the strains produced and is prototrophic for uracil, adenine, histidine, proline, arginine, and tryptophan. The strain is resistant to Zeocin and contains about three to four copies of the rhEPO expression cassette. The strain has a disruption or deletion of the BMT2 and BMT4 genes.

Plasmid pGLY3430 (pSH1115) (FIG. 16) is an integration vector that contains an expression cassette comprising a nucleic acid molecule encoding the Nourseothricin resistance (NAT^(R)) ORF (originally from pAG25 from EROSCARF, Scientific Research and Development GmbH, Daimlerstrasse 13a, D-61352 Bad Homburg, Germany, See Goldstein et al., Yeast 15: 1541 (1999)) ORF (SEQ ID NO:102) operably linked to the Ashbya gossypii TEF1 promoter (SEQ ID NO:105) and Ashbya gossypii TEF1 termination sequences (SEQ ID NO:106) flanked one side with the 5′ nucleotide sequence of the P. pastoris BMT1 gene (SEQ ID NO:68) and on the other side with the 3′ nucleotide sequence of the P. pastoris BMT1 gene (SEQ ID NO:69). Plasmid pGLY3430 was linearized and the linearized plasmid transformed into strain YGLY4439 to produce a number of strains in which the NATR expression cassette has been inserted into the BMT1 locus by double-crossover homologous recombination. The strain YGLY6661 was selected from the strains produced and is prototrophic for uracil, adenine, histidine, proline, arginine, and tryptophan. The strain is resistant to Zeocin and Nourseothricin and contains about three to four copies of the EPO expression cassette. The strain has a disruption or deletion of the BMT1, BMT2, and BMT4 genes. Strain YGLY7013 was selected as well; however, this strain had only a partial disruption of the BMT1 gene. This strain was designated as having a disruption or deletion of the BMT1, BMT2 and BMT4 genes.

Plasmid pGLY4472 (pSH1186) (FIG. 17) is an integration vector that contains an expression cassette comprising a nucleic acid molecule encoding the E. coli hygromycin B phosphotransferase gene (Hyg^(R)) ORF (SEQ ID NO:103) operably linked to the Ashbya gossypii TEF1 promoter (SEQ ID NO:105) and Ashbya gossypii TEF1 termination sequences (SEQ ID NO:106) flanked one side with the 5′ nucleotide sequence of the P. pastoris BMT3 gene (SEQ ID NO:70) and on the other side with the 3′ nucleotide sequence of the P. pastoris BMT3 gene (SEQ ID NO:71). Plasmid pGLY3430 was linearized and the linearized plasmid transformed into strain YGLY6661 to produce a number of strains in which the Hyg^(R) expression cassette has been inserted into the BMT3 locus by double-crossover homologous recombination. Strains YGLY7361 to YGLY7366 and strains YGLY7393 to YGLY7398 were selected from the strains produced and are prototrophic for uracil, adenine, histidine, proline, arginine, and tryptophan. The strains are resistant to Zeocin, Nourseothricin, and Hygromycin and contain about three to four copies of the EPO expression cassette. The strains have disruptions or deletions of the BMT1, BMT2, BMT3, and BMT4 genes and produce rhEPO lacking cross-reactivity binding to antibodies made against host cell antigen (HCA).

Example 3

Strain YGLY3159 in Example 1 was further genetically engineered to produce strains in which the BMT1, BMT3, and BMT4 genes have been disrupted or deleted and to include several copies of an expression cassette encoding mature human EPO fused to the chicken lysozyme leader peptide. Briefly, construction of these strains from YGLY3159 is shown in FIG. 1 and briefly described as follows.

Strain YGLY3159 was counterselected in the presence of 5-FOA to produce strain YGLY3225, which is now auxotrophic for uridine.

Plasmid pGLY2057 (FIG. 18) is an integration vector that targets the ADE2 locus and contains an expression cassette encoding the P. pastoris URA5 gene flanked by lacZ repeats. The expression cassette is flanked on one side by a nucleic acid molecule comprising a nucleotide sequence from the 5′ region of the ADE2 gene (SEQ ID NO:100) and on the other side by a nucleic acid molecule comprising a nucleotide sequence from the 3′ region of the ADE2 gene (SEQ ID NO:101). Plasmid pGLY2057 was linearized with SfiI and the linearized plasmid transformed into strain YGLY3225 to produce a number of strains in which the URA5 cassette has been inserted into the ADE2 locus by double-crossover homologous recombination. Strain YGLY3229 was selected from the strains produced and is auxotrophic for adenine and prototrophic for uridine, histidine, proline, arginine, and tryptophan. The strain is resistant to Zeocin and contains about three to four copies of the EPO expression cassette.

Plasmid pGLY2680 (FIG. 19) is an integration vector that can target the TRP2 or AOX1 locus and contains expression cassettes encoding (1) a chimeric EPO comprising the human mature erythropoetin (EPO) fused at the N-terminus to chicken lysozyme signal peptide to target the chimeric protein to the secretory pathway and secretion from the cell and (2) the P. pastoris ADE2 gene without a promoter. The ADE2 gene is poorly transcribed from a cryptic promoter. Thus, selection of ade2Δ yeast strains transformed with the vector in medium not supplemented with adenine requires multiple copies of the vector to be integrated into the genome to render the recombinant prototrophic for adenine. Since the vector further includes the EPO expression cassette, the recombinant yeast will also include multiple copies of the EPO cassette integrated into the genome. This vector and method has been described in Published PCT Application WO2009085135. The DNA sequence encoding the chicken lysozyme signal peptide is shown in SEQ ID NO:94, the codon-optimized ORF encoding the mature human EPO is shown in SEQ ID NO:92, and the P. pastoris ADE2 gene without its promoter but including its termination sequences is shown in SEQ ID NO:96. The chimeric EPO is operably linked to the AOX1 promoter and S. cerevisiae CYC termination sequences. The two tandem cassettes are flanked on one side by a nucleic acid molecule comprising a nucleotide sequence comprising the TRP2 gene.

Plasmid pGLY2680 was linearized at the PmeI site and transformed into YGLY3229 to produce a number of strains in which the two expression cassette have been inserted into the AOX1 locus by roll in single-crossover homologous recombination, which results in multiple copies of the EPO expression cassette inserted into the AOX1 locus without disrupting the AOX1 locus. Strain YGLY4209 was selected from the strains produced. This strain there are about 5-7 copies of the EPO expression cassette as determined by measuring the intensity of sequencing data of DNA isolated from the strain inserted into the locus. The strain is prototrophic for adenine, uridine, histidine, proline, arginine, and tryptophan. The strain contains in total about eight to eleven copies of EPO expression cassettes. During processing of the chimeric EPO in the ER and Golgi, the leader peptide is removed. Thus, the rhEPO produced is the mature form of the EPO.

Strain YGLY4209 was counterselected in the presence of 5′-FOA to produce a number of strains that were auxotrophic for uracil. From the transformants produced, strain YGLY4244 was selected.

Plasmid pGLY2713 (FIG. 20), an integration vector that targets the P. pastoris PEP4 gene (SEQ ID NO:104), contains the P. pastoris PNO1 ORF adjacent to the expression cassette comprising the P. pastoris URA5 gene flanked by lacZ repeats and flanked on one side with the 5′ nucleotide sequence of the P. pastoris PEP4 gene and on the other side with the 3′ nucleotide sequence of the P. pastoris PEP4 gene. Plasmid pGLY2713 was linearized with SfiI and the linearized plasmid transformed into strain YGLY4244 to produce a number of strains in which the PNO1 ORF and URA5 expression cassette have been inserted into the PEP4 locus by double-crossover homologous recombination. Strain YGLY5053 was selected from the strains produced and counterselected in the presence of 5-FOA to produce a number of strains in which the URA5 has been lost from the genome. Strain YGLY5597 was selected from the strains produced and is prototrophic for adenine, histidine, proline, arginine, and tryptophan. The strain is resistant to Zeocin and contains about eight to eleven copies of the rhEPO expression cassette.

Plasmid pGLY3411 (pSH1092) (FIG. 15) is an integration vector that contains the expression cassette comprising the P. pastoris URA5 gene flanked by lacZ repeats flanked on one side with the 5′ nucleotide sequence of the P. pastoris BMT4 gene (SEQ ID NO:72) and on the other side with the 3′ nucleotide sequence of the P. pastoris BMT4 gene (SEQ ID NO:73). Plasmid pGLY3411 was linearized and the linearized plasmid transformed into strain YGLY5597 to produce a number of strains in which the URA5 expression cassette has been inserted into the BMT4 locus by double-crossover homologous recombination. The strain YGLY5618 was selected from the strains produced and is prototrophic for uracil, adenine, histidine, proline, arginine, and tryptophan. The strain is resistant to Zeocin and Nourseothricin and contains about eight to eleven copies of the rhEPO expression cassette. The strain has disruptions of the BMT2 and BMT4 genes.

Plasmid pGLY3430 (pSH1115) (FIG. 16) is an integration vector that contains an expression cassette comprising a nucleic acid molecule encoding the Nourseothricin resistance (NATR) ORF (originally from pAG25 from EROSCARF, Scientific Research and Development GmbH, Daimlerstrasse 13a, D-61352 Bad Homburg, Germany, See Goldstein et al., Yeast 15: 1541 (1999)) ORF (SEQ ID NO:102) operably linked to the Ashbya gossypii TEF1 promoter and Ashbya gossypii TEF1 termination sequences flanked one side with the 5′ nucleotide sequence of the P. pastoris BMT1 gene (SEQ ID NO:68) and on the other side with the 3′ nucleotide sequence of the P. pastoris BMT1 gene (SEQ ID NO:69). Plasmid pGLY3430 was linearized and the linearized plasmid transformed into strain YGLY5618 to produce a number of strains in which the NATR expression cassette has been inserted into the BMT1 locus by double-crossover homologous recombination. The strain YGLY7110 was selected from the strains produced and is prototrophic for uracil, adenine, histidine, proline, arginine, and tryptophan. The strain is resistant to Zeocin and Nourseothricin and contains about eight to eleven copies of the rhEPO expression cassette. The strain has disruptions of the BMT1, BMT2, and BMT4 genes.

Plasmid pGLY4472 (pSH1186) (FIG. 17) is an integration vector that contains an expression cassette comprising a nucleic acid molecule encoding the E. coli hygromycin B phosphotransferase gene (Hyg^(R)) ORF (SEQ ID NO:103) operably linked to the Ashbya gossypii TEF1 promoter and Ashbya gossypii TEF1 termination sequences flanked one side with the 5′ nucleotide sequence of the P. pastoris BMT3 gene (SEQ ID NO:70) and on the other side with the 3′ nucleotide sequence of the P. pastoris BMT3 gene (SEQ ID NO:71). Plasmid pGLY3430 was linearized and the linearized plasmid transformed into strain YGLY7110 to produce a number of strains in which the Hyg^(R) expression cassette has been inserted into the BMT3 locus by double-crossover homologous recombination. Strains YGLY7113 to YGLY7122 were selected from the strains produced and are prototrophic for uracil, adenine, histidine, proline, arginine, and tryptophan. The strains are resistant to Zeocin, Nourseothricin, and Hygromycin and contain about eight to eleven copies of the EPO expression cassette. The strains have disruptions of the BMT1, BMT2, BMT3, and BMT4 genes and produce rhEPO lacking detectable cross-reactivity binding to antibodies made against HCA.

Example 4

Several of the strains in Examples 1 to 3 were used to produce rhEPO as described below and shown schematically in FIG. 21. Briefly, production begins by inoculating shake flasks containing culture media with cells from the working cell bank and proceeds through a series of inoculations, incubations, and transfers of the expanding cultures into vessels of increasing size until sufficient biomass is available to inoculate the production bioreactor. Glycerol is the primary carbon source during batch phase, then culture growth is maintained through feeding of glycerol and salts. When the glycerol is depleted, cells are induced to express rhEPO protein by switching to a methanol feed. Inhibitors are added at induction to minimize O-glycosylation (e.g., PMTi 3, 5-[[3-(1-Phenylethoxy)-4-(2-phenylethoxy)]phenyl]methylene]-4-oxo-2-thioxo-3-thiazolidineacetic Acid, (See Published PCT Application No. WO 2007061631)) and to minimize proteolysis. Inhibitors of proteolysis are added again at the end of the phase to minimize proteolysis. The culture is cooled to about 4° C. and harvested.

Laboratory scale cultivation of the strains was conducted in 500 mL SixFors and 3 L fermentors using in general the following procedures. Bioreactor Screenings (SIXFORS) are done in 0.5 L vessels (Sixfors multi-fermentation system, ATR Biotech, Laurel, Md.) under the following conditions: pH at 6.5, 24° C., 0.3 SLPM, and an initial stirrer speed of 550 rpm with an initial working volume of 350 mL (330 mL BMGY medium and 20 mL inoculum). IRIS multi-fermenter software (ATR Biotech, Laurel, Md.) is used to linearly increase the stirrer speed from 550 rpm to 1200 rpm over 10 hours, one hour after inoculation. Seed cultures (200 mL of BMGY in a 1 L baffled flask) are inoculated directly from agar plates. The seed flasks are incubated for 72 hours at 24° C. to reach optical densities (OD₆₀₀) between 95 and 100. The fermenters are inoculated with 200 mL stationary phase flask cultures that were concentrated to 20 mL by centrifugation. The batch phase ended on completion of the initial charge glycerol (18-24 h) fermentation and are followed by a second batch phase that is initiated by the addition of 17 mL of glycerol feed solution (50% [w/w] glycerol, 5 mg/L Biotin, 12.5 mL/L PMTi salts (65 g/L FeSO₄.7H₂O, 20 g/L ZnCl₂, 9 g/L H₂SO₄, 6 g/L CuSO₄.5H₂O, 5 g/L H₂SO₄, 3 g/L MnSO₄.7H₂O, 500 mg/L CoCl₂.6H₂O, 200 mg/L NaMoO₄.2H₂O, 200 mg/L biotin, 80 mg/L NaI, 20 mg/L H₃BO₄)). Upon completion of the second batch phase, as signaled by a spike in dissolved oxygen, the induction phase is initiated by feeding a methanol feed solution (100% MeOH 5 mg/L biotin, 12.5 mL/L PMTi) at 0.6 g/h for 32-40 hours. The cultivation is harvested by centrifugation.

Bioreactor cultivations (3 L) are done in 3 L (Applikon, Foster City, Calif.) and 15 L (Applikon, Foster City, Calif.) glass bioreactors and a 40 L (Applikon, Foster City, Calif.) stainless steel, steam in place bioreactor. Seed cultures are prepared by inoculating BMGY media directly with frozen stock vials at a 1% volumetric ratio. Seed flasks are incubated at 24° C. for 48 hours to obtain an optical density (OD₆₀₀) of 20±5 to ensure that cells are growing exponentially upon transfer. The cultivation medium contained 40 g glycerol, 18.2 g sorbitol, 2.3 g K₂HPO₄, 11.9 g KH₂PO₄, 10 g yeast extract (BD, Franklin Lakes, N.J.), 20 g peptone (BD, Franklin Lakes, N.J.), 4×10⁻³ g biotin and 13.4 g Yeast Nitrogen Base (BD, Franklin Lakes, N.J.) per liter. The bioreactor is inoculated with a 10% volumetric ratio of seed to initial media. Cultivations are done in fed-batch mode under the following conditions: temperature set at 24±0.5° C., pH controlled at to 6.5±0.1 with NH₄OH, dissolved oxygen was maintained at 1.7±0.1 mg/L by cascading agitation rate on the addition of O₂. The airflow rate is maintained at 0.7 vvm. After depletion of the initial charge glycerol (40 g/L), a 50% glycerol solution containing 12.5 mL/L of PTM1 salts is fed exponentially at 50% of the maximum growth rate for eight hours until 250 g/L of wet cell weight was reached. Induction is initiated after a 30 minute starvation phase when methanol was fed exponentially to maintain a specific growth rate of 0.01 h⁻¹. When an oxygen uptake rate of 150 mM/L/h is reached the methanol feed rate is kept constant to avoid oxygen limitation. The cultivation is harvested by centrifugation.

After clarification by centrifugation and microfiltration, the filtrate is concentrated 10× by ultrafiltration and the rhEPO protein is purified through a sequence of two chromatography steps using a blue dye-affinity and hydroxyapatite.

Primary clarification is performed by centrifugation. The whole cell broth is transferred into 1000 mL centrifuge bottles and centrifuged at 4° C. for 15 minutes at 13,000×g. An ultrafiltration step can be employed for larger fermentors (10 L to 40 L and larger). This step can be performed utilizing Sartorious flat sheets with a pore size of 10K to a five-fold concentration.

A capture step is performed using Blue SEPHAROSE 6 Fast Flow (Pseudo-Affinity) Chromatography. A Blue SEPHAROSE 6 fast Flow (FF) column (GE Healthcare) is equilibrated with 50 mM MOPS, pH 7.0. The culture supernatant is adjusted to 100 mM NaCl and passed through dead-end filter (Whatman, Polycap TC) before loading to the column. The residence time is maintained to about 10 minutes with a 3 column volumes (CV) wash after loading. The elution is step elution of 4 CV with 1 M NaCl in 50 mM MOPS, pH 7.0. EPO elutes at the 1 M NaCl.

An intermediate step is performed using hydroxyapatite (HA) chromatography. A Macro-prep ceramic hydroxyapatite Type I 40 μm (Bio-Rad) is used after the capture step. This column is equilibrated with equilibration solution: 50 mM MOPS, pH 7.0 containing 1 M NaCl and 10 mM CaCl₂. About 10 mM CaCl₂ is added to the pooled rhEPO from the blue column before loading. The column wash is executed with 3 CV of equilibration solution followed by step elution of 10 CV at 12.5 mM Na phosphate in MPOS, pH 7.0 to provide HA pool 1 containing the rhEPO.

A cation exchange chromatography step can be used to further purify the rhEPO. The pooled sample after hydroxyapatite chromatography step (e.g., HA pool 1) is dialyzed against 50 mM Na acetate, pH 5.0 overnight at 4° C. and a Source 30S column or Poros cation exchange column (GE Healthcare) is equilibrated with the same buffer. The dialyzed sample is applied to the column and a 10 CV linear gradient from 0 to 750 mM NaCl is applied with rhEPO eluting between 350 to 500 mM NaCl to provide the rhEPO.

The N terminus of the purified rhEPO molecule can be conjugated to 40-kDa linear polyethylene glycol (PEG) via reductive amination (PEGylation). The activated PEG is added to the rhEPO sample (conc. about 1 mg/mL) in 50 mM Sodium acetate buffer at pH 5.2 at a protein:PEG ratio of 1:10. The reaction is carried out at room temperature under reducing conditions by adding 10 mM sodium cyanoborohydride to the reaction mixture with overnight stirring. The reaction is stopped by adding 10 mM Tris, pH 6.0.

The mono-PEGylated rhEPO product is purified using a cation-exchange chromatography step before diafiltration into the final formulation buffer (20 mM sodium phosphate, 120 mM sodium chloride, 0.005% Polysorbate 20 (w/v), pH 7.0).

The final product is diluted to a concentration suitable for filling and sterile filtered into the drug substance storage container. The PEGylated rhEPO can be stored at 2-8° C. until filling, at which time it is aseptically filled into glass vials that are then sealed with a rubber stopper and aluminum cap.

Commercial formulations of proteins are known and may be used. Examples include but are not limited to ARANESP®: Polysorbate solution: Each 1 mL contains 0.05 mg polysorbate 80, and is formulated at pH 6.2±0.2 with 2.12 mg sodium phosphate monobasic monohydrate, 0.66 mg sodium phosphate dibasic anhydrous, and 8.18 mg sodium chloride in water for injection, USP (to 1 mL). Albumin solution: Each 1 mL contains 2.5 mg albumin (human), and is formulated at pH 6.0±0.3 with 2.23 mg sodium phosphate monobasic monohydrate, 0.53 mg sodium phosphate dibasic anhydrous, and 8.18 mg sodium chloride in water for injection, USP (to 1 mL). EPOGEN® is formulated as a sterile, colorless liquid in an isotonic sodium chloride/sodium citrate buffered solution or a sodium chloride/sodium phosphate buffered solution for intravenous (IV) or subcutaneous (SC) administration. Single-dose, Preservative-free Vial: Each 1 mL of solution contains 2000, 3000, 4000 or 10,000 Units of Epoetin alfa, 2.5 mg Albumin (Human), 5.8 mg sodium citrate, 5.8 mg sodium chloride, and 0.06 mg citric acid in water for injection, USP (pH 6.9±0.3). This formulation contains no preservative. Preserved vials contain 1% benzyl alcohol.

Example 5

Methods used for analyzing the presence or absence of host cell antigen (HCA) included Western blot analysis and sandwich enzyme-linked immunosorbent assay (ELISA).

Host cell Antigen (HCA) antibody was prepared in rabbits using the supernatant from NORF strain cultures. The NORF strain is genetically the same as YGLY3159 except that it lacks the ORF encoding the human mature EPO. NORF strain fermentation supernatant prepared in complete Freund's adjuvant was injected into rabbits, which were then boosted three times with fermentation supernatant prepared in Incomplete Freund's adjuvant. After 45 days, the rabbits were bled and polyclonal antibodies to HCA were prepared using standard methods, for example, rabbit polyclonal IgG 9161 F072208-S, which was SLr Protein A purified, and GiF2 polyclonal rabbit::6316 whole rabbit serum. The GIF2 antibody was not protein A purified.

Western Blots for detecting P. Pastoris HCA were performed as follows. Purified PEGylated or non-PEGylated rhEPO-containing samples were reduced in sample loading buffer, of which 1 μL was then applied to the wells of 4-20% polyacrylamide SDS Tris-HCl (4-20% SDS-PAGE) gels (Bio RAD) and electrophoresed at 150V for about 60 minutes. The resolved proteins were electrotransferred to nitrocellulose membranes at 100V for about 60 minutes. After transfer, the membranes were blocked for one hour with 1% Blocking Solution (Roche Diagnostics). After blocking, the membranes were probed with the rabbit anti-HCA polyclonal antibody (primary antibody) diluted 1:3000. Afterwards, the membranes were washed and detection of the rabbit anti-HCA antibody was with the secondary antibody, goat-anti-Rabbit IgG (H+L) (Pierce #31460, Lot #H51015156) conjugated to horseradish peroxidase (HRP), at a 1:5000 dilution. After washing the membranes, detection of bound secondary antibody was using 3,3′ Diaminobenzidine (DAB). For detecting EPO protein, the primary antibody was EPO (B-4) HRP-conjugated antibody used at a 1:1000 dilution (SC5290 Lot#A0507, Santa Cruz Biotechnology). A secondary antibody was not used. Routinely, the EPO samples were electrophoresed in parallel with rhEPO samples that had been deglycosylated with PNGaseF treatment. Deglycosylation was performed with 50 uL samples to which 1 μL of PNGaseF enzyme at 500 units/uL was added. After incubation at 37° C. for two hours, the samples were reduced in sample loading buffer and 1 μL aliquots were removed and applied to the SDS gels as above.

Sandwich ELISAs for detecting P. Pastoris HCA were performed as follows. The wells of 96 well ELISA plates were coated with 1 μg/well of mouse anti-hEPO monoclonal antibody. The wells were then blocked for 30 minutes with phosphate-buffered saline (PBS). About 100 μL of purified non-PEGylated rhEPO-containing samples concentrated to about 200 ng/mL were added to the wells. Primary detection used the rabbit anti-HCA polyclonal antibody at a 1:800 starting dilution in PBS which was then serially diluted 1:1 in PBS across a row ending with the 11^(th) well at a 1:819, 200 dilution. The 12^(th) well served as a negative control. The standard for the ELISA was rhEPO purified from YGLY3159. After 60 minutes, the wells were washed with PBS three times. Detection of the rabbit anti-HCA antibody used goat anti-rabbit antibody conjugated to alkaline phosphatase (AP) at a 1:10,000 dilution in PBS. After 60 minutes the wells were washed three times with PBS and detection of bound secondary antibody used 4-Methylumbelliferyl phosphate (4-MUPS). The ELISA plates were read using a Tecan Genios Multidetection Microplate Reader at 340 nm excitation wavelength and 465 nm emission wavelength.

Example 6

This example shows that YGLY3159 produces rhEPO with cross binding activity (CBA) with anti-HCA antibody and that the cross-binding activity was due to the presence of β-1,2-mannose residues (α-1,2-mannosidase resistant) on at least a portion of the N-glycans on the rhEPO even though the rhEPO had been produced in strain in which the β-1,2-mannosyltransferase gene BMT2 had been deleted or disrupted.

rhEPO was recovered by a three-step chromatographic separation from the fermentation supernatant of glyco-engineered P. pastoris production strain YGLY 3159 showed about 95% protein purity as determined by SDS-PAGE, RP-HPLC, and SEC-HPLC. Mono-PEGylated rhEPO was separated by cation-exchange chromatographic step from its hyper and un-PEGylated conjugates with about 96% purity as determined by SDS-PAGE gel. However, antibody against HCA of the YGLY3159 strain detected a glycoprotein in rhEPO preparations produced from the strain that co-migrated with rhEPO on Western blots. FIG. 22 which shows that anti-HCA antibody identified a protein that co-migrates with rhEPO on 4-20% SDS-PAGE gels. Removal of sialic acid from rhEPO did not abolish the cross-binding activity; however, removal of the entire N-glycan from rhEPO using PNGase F produced a deglycosylated form of rhEPO that was not detectable in Western blots probed with anti-HCA antibody. This is shown in FIG. 23 which shows that only the deglycosylated form of rHEPO lacked cross-binding activity with the anti-HCA antibody.

To determine wither the cross-binding activity was rhEPO specific or could be identified in purified glycoprotein preparations from other recombinant P. pastoris strains, an glycoproteins produced in other strains were isolated, resolved by 4-20% SDS-PAGE gels, and the gels transferred to nitrocellulose membranes. In the case of a recombinant human whole antibody (rhIgG) produced in a recombinant P. pastoris, cross-binding activity was detected in protein preparations produced in wild-type P. pastoris (hypermannosylated from both N and O-glycosylated region) and in a recombinant GS2.0 strain that makes predominantly Man₅GlcNAc₂ N-glycans but also contained detectable Man₉GlcNAc₂ N-glycans that were α-1,2-mannosidase resistant (FIG. 24, arrow). However, the rhIgG preparations from wild-type P. pastoris contained cross-binding activity with an apparent molecular weight greater than that of rhIgG suggesting that the preparations contained contaminating host cell glycoproteins. The cross-binding activity was not removed by PNGase F digestion (circled in FIG. 24).

FIG. 25 shows that glycosylated rhEPO produced in YGLY3159 had cross binding activity to anti-HCA antibody but that human fetuin, human asialofetuin, human serum albumin (HSA), and LEUKINE (a recombinant human granulocyte macrophage colony stimulating factor (rhu GM-CSF) produced in S. cerevisiae) had no cross-binding activity to anti-HCA antibody. Fetuins are heavily glycosylated blood glycoproteins that are made in the liver and secreted into the blood stream. They belong to a large group of binding proteins mediating the transport and availability of a wide variety of cargo substances in the blood stream. The best known representative of these carrier proteins is serum albumin, the most abundant protein in the blood plasma of adult animals. Fetuin is more abundant in fetal blood, hence the name “fetuin” (from Latin, fetus). Fetal calf serum contains more fetuin than albumin while adult serum contains more albumin than fetuin. Asialofetuins are fetuins which the terminal sialic acid from N- and O-glycans are removed by mild hydrolysis or neuraminidase treatment. Currently, there are no reports of β-linked mannoses in S. cerevisiae. HSA is not a glycosylated protein.

Lab scale data demonstrated that the intermediate chromatographic step purification of rhEPO from Blue SEPHAROSE 6 FF capture pool using hydroxy apatite (HA) type I 40 μm resin can separate rhEPO that has nearly undetectable cross-binding activity (HA pool 1) from rhEPO that had high-mannose-type N-glycans (HA pools 2 and 3). HA pool 1 contained about 90.40% bisialylated N-glycans (the desired N-glycan form) and less than 3.5% neutral N-glycans. In contrast, linear gradient elution from 0 to 100 mM sodium phosphate showed that later elution fractions (HA pools 2 and 3) contained high mannose-type N-glycans and increased cross binding activity to anti-HCA antibody in Western blots. This can be seen in the HPLC N-glycan analysis and Western blots of 4-20% SDS-PAGE gels shown in FIG. 26

Anion column chromatography using Q SEPHAROSE FF or Source 30Q anion resins were also tested. The HA pools 1-3 were combined and dialyzed against 50 mM Na acetate, pH 5.0 overnight at 4° C. The dialyzed sample was applied to the column and a 10 CV linear gradient from 0 to 750 mM NaCl was applied with rhEPO eluting between 350 to 500 mM NaCl to provide the rhEPO. FIG. 27A shows an example of a Q SEPHAROSE FF purification of rhEPO. Data showed that high mannose type glycans (Man_(6,7,8,9,>9), mostly α 1,2 mannosidase resistant) that show corresponding higher cross-binding activity did not bind to the anion exchange resins when bound and unbound material was analyzed in a sandwich ELISA (FIG. 27B). Table 1 shows the results of HPLC analysis of the N-glycan content of the rhEPO in the bound fraction (Q SEPHAROSE FF pool 1) and flow-through fraction (Q SEPHAROSE FF Flow Through). Table 2 shows the N-glycan content of the neutral N-glycans shown in Table 1.

TABLE 1 Q Sepharose FF - Purification of rhEPO N-Glycan HPLC Analysis % Mono % Bi Sample % Neutral Sialylated Sialylated Input (HA pools) 11.04 13.66 75.30 Q SEPHAROSE FF pool 1 3.01 6.47 90.52 Q SEPHAROSE FF Flow 26.71 21.19 52.10 Through

TABLE 2 Q Sepharose FF - Purification of rhEPO % Neutral N-Glycan Profile Sample % G2 % Man₅ % Man₆₋₈ % Man₉ Input (HA pools) 3.1 2.8 2.4 2.74 Q SEPHAROSE FF pool 1 3.01 ND ND ND Q SEPHAROSE FF Flow Through 4.2 8.0 3.9 10.61 ND—not detected G2—N-glycan structure is Gal₂GlcNAc₂Man₃GlcNAc₂

The figures and tables show that rhEPO with undetectable cross-binding activity to anti-HCA antibodies and good protein and glycan quality can therefore be bound/eluted from anion exchange resins. These data also suggested that the family of fungal genes involved in biosynthesis of β-1,2-linked oligomannosides (BMT1, BMT2, BMT3, BMT4) was responsible for the low level cross-binding impurities in the rhEPO preparations.

Therefore, when viewed as a whole, the results suggested that the cross-binding activity to anti-HCA antibodies was not specific to rhEPO but was due to α-1,2-mannosidase resistant N-glycans on the glycoproteins. YGLY 3159 had been generated by knocking out five endogenous glycosylation genes and introducing 15 heterologous genes. YGLY3159 is bmt2Δ knockout strain. NMR spectroscopy studies suggest that bmt2Δ knockout strains can produce glycoproteins with varying amounts of residual β-1,2-mannose N-glycans. Since YGLY 3159 is bmt24, it was postulated that BMT1 and BMT3 were responsible for the residual low level β-1,2-mannose transfer on core N-glycans.

While a combination of chromatography steps to purify the rhEPO can produce rhEPO preparations free of detectable cross-binding activity to anti-HCA antibodies, it would be particularly desirable to genetically modify the P. pastoris host strains to reduce or eliminate detectable cross-binding activity to anti-HCA antibodies in the strains. This minimizes the risk of possible contamination of the rhEPO preparations with cross-binding activity due to variability during the purification. In addition, because each purification step can result in a loss of rhEPO, the genetically modified P. pastoris strains can reduce the number of purification steps and thus reduce the amount of rhEPO lost during the steps eliminated. Therefore, expression of the four BMT genes were serially deleted or disrupted to identify strains that did not produce detectable cross-binding activity to anti-HCA antibodies.

Example 7

In order to reduce the presence of β-linked mannose type N-glycans to undetectable levels, the BMT1 and BMT4 genes were disrupted and the rhEPO analyzed for the presence of α-1,2-mannosidase resistant N-glycans.

Strains YGLY6661 and YGLY7013 were constructed as described Example 2 and analyzed for the presence of α-1,2-mannosidase resistant N-glycans using anti-HCA antibodies. Strain YGLY7013 was bmt2Δ and bmt44 and strain YGLY6661 was bmt2Δ, bmt4Δ, and bmt1Δ. rhEPO produced from the strains were subjected Blue SEPHAROSE 6FF chromatography and aliquots of the Blue SEPHAROSE 6FF capture pool were treated with PNGase F vel non. The treated and untreated aliquots were electrophoresed on SDS-PAGE, the gels transferred to nitrocellulose membranes, and the membranes probed with anti-EPO antibody or anti-HCA antibodies. FIG. 28 shows in Western blots of 4-20% SDS-PAGE gels of aliquots of Blue SEPHAROSE 6 FF capture pools that rhEPO produced in either strain still had α-1,2-mannosidase resistant N-glycans which cross-reacted with anti-HCA antibodies. Tables 3 and 4 show the distribution of N-glycan species in rhEPO in Blue Sepaharose 6 FF capture pools from both fermentation and SixFors cultures. As shown in the tables, both strains produced a substantial amount of neutral N-glycans of which a portion was resistant to in vitro α1,2-mannosidase digestion.

TABLE 3 Week 44 - rhEPO - Blue SEPHAROSE 6 FF Capture Pool - Fermentation % Bi- % Mono % % Neutral Pools Sialylated Sialylated Neutral % G2 % M5 % M6-M8 % M9+ F074411 52.98 34.08 12.94 1.7 2.63 3.65 4.96 (YGLY 6661) F074411 53.42 34.32 12.26 1.9 5.05 3.4 1.91 (YGLY 6661) α1,2 Mannosidase F074410 25.10 47.00 27.90 12.99 2.22 5.67 7.02 (YGLY 7013) F074410 26.34 49.03 26.34 13.14 5.39 4.68 1.42 (YGLY 7013) α1,2 Mannosidase G2—Gal₂GlcNAc₂Man₃GlcNAc₂ N-glycans M6-M8—Man₆GlcNAc₂ to Man₈GlcNAc₂ N-glycans M9+—Man₉GlcNAc₂ and lager N-glycans

TABLE 4 Week 41 - rhEPO - Blue SEPHAROSE 6 FF Capture Pool - SixFors % Bi- % Mono % % Neutral Pools Sialylated Sialylated Neutral % G2 % M5 % M6-M8 % M9 % M9+ X074128 43.49 39.24 17.27 1.7 7.8 6.69 0.45 0.63 (YGLY 6661) X074128 42.52 39.26 18.22 1.2 11.84 5.02 0.1 0.06 (YGLY 6661) α1,2 Mannosidase X074131 66.90 18.83 14.27 1.84 8.36 2.82 0.66 0.59 (YGLY 7013) X074131 64.81 19.70 15.49 1.06 13.1 0.77 0.56 0 (YGLY 7013) α1,2 Mannosidase G2—Gal₂GlcNAc₂Man₃GlcNAc₂ N-glycans M6-M8—Man₆GlcNAc₂ to Man₈GlcNAc₂ N-glycans M9—Man₉GlcNAc₂ N-glycans M9+—Man₉GlcNAc₂ and lager N-glycans A sandwich ELISA of rhEPO in the Blue SEPHAROSE 6 FF capture pools made from both strains compared to YGLY3159 showed that both strains had cross-binding activity to anti-HCA antibody (FIG. 29). Further purifying the rhEPO by hydroxyapatite (HA) chromatography and analyzing the samples by sandwich ELISA showed that the HA pool 1 containing rhEPO produced from YGLY6661 (bmt2Δ, bmt4Δ, and bmt1Δ) appeared to lack detectable cross-binding activity to anti-HCA antibody but that rhEPO produced in YGLY7013 (bmt2Δ and bmt4Δ) still had detectable cross-binding activity to anti-HCA antibody (FIG. 30). The results suggested that deleting the BMT2 and BMT1 genes was not sufficient to remove all detectable cross-binding activity. The results also show that hydroxyapatite chromatography can remove detectable cross-binding activity in the HA pool 1. FIG. 31 is a Western blot of 4-20% SDS-PAGE gels showing that rhEPO in another Blue SEPHAROSE 6 FF capture pool prepared from strain YGLY6661 continued to have cross-binding activity to anti-HCA antibody and that the cross-binding activity could be still be rendered undetectable by deglycosylating the rhEPO. The result indicated that to produce rhEPO that had no detectable cross-binding activity to anti-HCA antibodies, expression of the BMT3 gene needed to be abrogated by disruption or deletion.

Example 8

In order to more effectively achieve the elimination of detectable β-linked mannose type glycans, all four BMT genes involved in -mannosyltransferase pathway were disrupted. Strains YGLY7361-7366 and YGLY7393-7398 (Example 2) were evaluated for ability to produce rhEPO lacking detectable cross-binding activity to anti-HCA antibody.

Various YGLY7361-7366 and YGLY7393-7398 strains in which all four BMT genes involved in the β-mannosyltransferase pathway were disrupted were grown in 500 mL SixFors fermentors and then processed for rhEPO through Blue SEPHAROSE 6 FF pools (Blue pools). Aliquots from the Blue pools were analyzed by 4-20% SDS-PAGE. FIG. 32 shows Commassie blue stained 4-20% SDS-PAGE gels of the Blue pools from the various strains with and without PNGase F treatment. The gels show that all of the tested strains produced glycosylated rhEPO. Several of the strains were evaluated for cross-binding activity to anti-HCA antibody by sandwich ELISA. FIG. 33 shows that most of the strains lacked detectable cross-binding activity to anti-HCA antibody. However, strains YGLY7363 and YGLY7365 had detectable cross-binding activity to anti-HCA antibody. Reconfirmation of YGLY7365 by PCR indicated that this strain was not a complete knock-out of the BMT3 gene, explaining the relatively high binding observed with the anti-HCA antibody present in the ELISA (FIG. 33). HPLC N-glycan analysis of strains YGLY7361-7366 is shown in Table 5 and strains YGLY7393-7398 are shown in Table 6. The data in the tables are graphically presented in FIG. 34.

TABLE 5 Week 46a - SixFors - Δbmt1-4 strains - Blue pools % Bi- % Mono % % Neutral Pools Sialylated Sialylated Neutral % G2 % M5 % M6-M8 % M9+ X074613 22.10 47.83 30.07 13.85 2.53 6.77 6.92 (YGLY 7361) X074613 21.55 48.18 30.27 13.68 4.53 5.47 6.59 (YGLY 7361) α1,2 Mannosidase X074614 67.36 24.69 7.95 0.6 4.36 2.8 0.19 (YGLY 7362) X074614 66.21 25.25 8.54 1.1 6.7 0.68 0.06 (YGLY 7362) α1,2 Mannosidase *X074615 49.40 39.17 11.43 0.8 4.42 5.91 0.3 (YGLY 7363) X074615 48.52 39.20 12.28 0.4 7.2 4.68 ND (YGLY 7363) α1,2 Mannosidase X074616 55.99 33.85 10.16 0.8 3.73 4.94 0.69 (YGLY 7366) X074616 55.44 34.24 10.32 1.9 7.2 1.02 0.2 (YGLY 7366) α1,2 Mannosidase *X074617 43.22 42.10 14.68 5.37 5.88 3.03 0.4 (YGLY 7365) X074617 42.70 42.40 14.90 4.5 8.4 2.0 ND (YGLY 7365) α1,2 Mannosidase X074618 48.18 38.44 13.38 0.7 6.56 5.76 0.36 (YGLY 7364) X074618 47.52 39.75 12.73 0.4 6.74 5.09 0.5 (YGLY 7364) α1,2 Mannosidase G2—Gal₂GlcNAc₂Man₃GlcNAc₂ N-glycans M6-M8—Man₆GlcNAc₂ to Man₈GlcNAc₂ N-glycans M9+—Man₉GlcNAc₂ and lager N-glycans *Showed cross-binding activity to anti-HCA antibody

TABLE 6 Week 46a - SixFors - Δbmt1-4 strains - Blue pools % Bi- % Mono % % Neutral Pools Sialylated Sialylated Neutral % G2 % M5 % M6-M8 % M9 % Hyb X074637 51.04 35.45 13.51 2.3 6.4  1.41 1.2 2.2 (YGLY 7393) X074637 50.33 35.44 14.23 2.5 9.14 ND ND 2.54 (YGLY 7393) α1,2 Mannosidase X074638 63.56 25.65 10.79 1.1 6.6 1.9 0.4 0.79 (YGLY 7394) X074638 62.88 25.75 11.37 1.2 8.96 ND ND 1.21 (YGLY 7394) α1,2 Mannosidase X074639 56.05 31.43 12.52 1.9 5.1 2.2 1.9 1.4 (YGLY 7395) X074639 56.27 31.81 11.92 1.9 8.43 ND ND 1.59 (YGLY 7395) α1,2 Mannosidase X074640 50.42 36.71 12.87 3.2 6.7  1.27 0.3 1.4 (YGLY 7396) X074640 49.94 36.86 13.20 3.2 8.12 ND ND 1.88 (YGLY 7396) α1,2 Mannosidase X074641 49.32 36.07 14.61 2.6 7.0 2.4 0.5 2.11 (YGLY 7397) X074641 48.72 35.86 15.42 2.7 10.24 ND ND 2.48 (YGLY 7397) α1,2 Mannosidase X074642 65.74 22.61 11.65 0.8 7.7  1.97  0.43 3.71 (YGLY 7398) X074642 64.99 22.87 12.14 1.0 10.02 ND ND 1.12 (YGLY 7398) α1,2 Mannosidase G2—Gal₂GlcNAc₂Man₃GlcNAc₂ N-glycans M6-M8—Man₆GlcNAc₂ to Man₈GlcNAc₂ N-glycans M9—Man₉GlcNAc₂ N-glycans M9+—Man₉GlcNAc₂ and lager N-glycans Hyb—hybrid N-glycans

Strains YGLY7362, 7366, 7396, and 7398 were cultivated in 3 L fermentors and processed through Blue SEPHAROSE 6 FF chromatography followed by hydroxyapatite (HA) chromatography. Aliquots from both the Blue pools and the HA pools were reduced and analyzed by 4-20% SDS-PAGE. Corresponding pools for YGLY3159 were included as positive controls. FIG. 35A shows a Commassie blue stained 4-20% SDS-PAGE showing that both the Blue pools (left half of gel) and HA pools (right half of gel) produced rhEPO. FIG. 35B shows a Western blot of the same samples probed with anti-HCA antibodies. None of the tested strains had any detectable cross-binding activity to anti-HCA antibodies in either the Blue pool or the HA pool 1.

FIG. 36 analyzes the Blue pool and HA pool 1 for rhEPO isolated from 500 mL SixFors cultures of YGLY7398 for cross-binding activity to anti-HCA antibodies. The right-most panel shows a Western blot probed with another anti-HCA preparation: GiF2 polyclonal rabbit::6316. This antibody produced the same results as produced using the F072208-S antibody, which had been used to produce the ELISAs and Western blots shown herein. The 6316 antibody shows that the cross-binding activity is not antibody specific.

These results show that deleting or disrupting all four BMT genes can result in strains that do not produce detectable cross-binding activity to anti-HCA antibodies in either the rhEPO after the preliminary Blue SEPHAROSE 6 FF capture step or the intermediate hydroxyapatite step using Type I 40 μM hydroxyapatite. These strains minimize the risk that rhEPO preparations will be made that contain cross-binding activity to anti-HCA antibodies. This enables the production of rhEPO with less risk of inducing an adverse immune response in the individual receiving the rhEPO.

Example 9

A comparison of the pharmacokinetics of the rhEPO produced in the strains produced in Example 2 with all four BMT genes disrupted or deleted and PEGylated was compared to PEGylated rhEPO produced from strain YGLY3159. The comparison showed that the PEGylated EPO had a reduced in vivo half-life and lower in vivo potency (See Tables 7 and 8). The rhEPO produced in the strains produced in Example 2 with no detectable cross-binding activity to anti-HCA antibodies had pharmacokinetics generally similar to that of EPOGEN and not the higher pharmacokinetics of ARANESP. The reduced pharmacokinetics was found to be a function of the amount of bi-sialylated biantennary N-glycans. Higher levels of bi-sialylated biantennary N-glycan on the rhEPO was correlated with higher pharmacokinetics. These results are consistent with published data showing that longer half life is correlated with greater sialic acid content in recombinant human erythropoietin produced in CHO cells (Egrie et al, Exp. Hematol. 31: 290-299 (2003)).

TABLE 7 PK of rhEPO from YGLY3159 (CBA) vs YGLY7398 (no CBA) YGLY3159 YGLY7398 T½ (hr) 20.9 ± 2 13 ± 2 CBA—cross-binding activity

TABLE 8 Relative Potency 95% rhEPO source (Reticulocyte Production) Confidence Interval YGLY3159 vs 0.82 (0.68, 1.00) YGLY7398

Example 10

In order to effectively achieve the elimination of detectable β-linked mannose type glycans and produce a strain that produces rhEPO with higher pharmacokinetics, strains YGLY7113-7122 described in Example 3 were made and evaluated for ability to produce rhEPO lacking detectable cross-binding activity to anti-HCA antibody. These strains were modified to also express human mature EPO as a fusion protein fused to the chicken lysozyme leader sequence. Thus, these strains express both human mature EPO fused to the S. cerevisiae αMATpre signal peptide and the human mature EPO as a fusion protein fused to the chicken lysozyme leader sequence.

Various YGLY7113-YGLY7122 strains in which all four BMT genes involved in the β-mannosyltransferase pathway were disrupted and expressing the were grown in 500 mL SixFors fermentors and then processed for rhEPO through Blue SEPHAROSE 6 FF pools (Blue pools). Aliquots of the Blue pools for several strains were analyzed by sandwich ELISA using anti-HCA antibodies. FIG. 37 shows that YGLY7118 had very low cross-binding activity to anti-HCA antibody but all of the other strains showed no detectable cross-binding activity to anti-HCA antibodies. HPLC N-glycan analysis of strains YGLY7113-7117 is shown in Table 9 and strains YGLY7118-7122 are shown in Table 10. The tables are graphically presented in FIG. 38.

TABLE 9 Week 48 - SixFors - Δbmt1-4 strains - Blue pools % Bi- % Mono % % Neutral Pools Sialylated Sialylated Neutral % G2 % M5 % M6-M8 % M9 % Hyb X074814 70.23 9.97 19.80 0.2 9.2 6.85 2.05 1.5 (YGLY 7113) X074814 68.96 10.56 20.48 0.3 18.4 ND ND 1.78 (YGLY 7113) α1,2 Mannosidase X074815 62.61 14.01 23.38 0.5 7.15 10.37  3.96 1.4 (YGLY 7115) X074815 61.77 13.95 24.28 0.1 22.22 ND ND 1.96 (YGLY 7115) α1,2 Mannosidase X074816 67.64 8.22 24.14 0.2 4.2 11.41  6.33 2.0 (YGLY 7114) X074816 65.92 8.32 25.76 0.2 23.35 ND ND 2.21 (YGLY 7114) α1,2 Mannosidase X074817 66.46 8.06 25.48 4.73 5.38 6.94 7.23 1.2 (YGLY 7116) X074817 65.54 8.69 25.77 0.5 23.8 ND ND 1.47 (YGLY 7116) α1,2 Mannosidase X074818 70.06 11.09 18.85 0.6 8.59 6.0  2.21 1.45 (YGLY 7117) X074818 68.67 11.42 19.91 0.4 17.5 ND ND 2.01 (YGLY 7117) α1,2 Mannosidase G2—Gal₂GlcNAc₂Man₃GlcNAc₂ N-glycans M6-M8—Man₆GlcNAc₂ to Man₈GlcNAc₂ N-glycans M9—Man₉GlcNAc₂ N-glycans M9+—Man₉GlcNAc₂ and larger N-glycans Hyb—hybrid N-glycans

TABLE 10 Week 48 - SixFors - Δbmt1-4 strains - Blue pools % Bi- % Mono % % Neutral Pools Sialylated Sialylated Neutral % G2 % M5 % M6-M8 % M9 % Hyb X074819 58.12 27.10 14.78 0.7 6.83 4.98 1.17 1.1 (YGLY 7119) X074819 57.03 26.87 16.10 0.45 14.55 ND ND 1.1 (YGLY 7119) α1,2 Mannosidase X074820 73.60 10.84 15.56 0.89 8.6 3.75 1.64 0.68 (YGLY 7120) X074820 72.43 11.13 16.44 0.7 15.63 ND ND 0.11 (YGLY 7120) α1,2 Mannosidase X074821 59.41 19.85 20.74 0.8 3.04 10.7  5.55 0.65 (YGLY 7121) X074821 58.39 20.00 21.6 0.4 20.17 ND ND 1.04 (YGLY 7121) α1,2 Mannosidase X074822 57.43 24.16 18.41 1.37 10.89 4.95 0.4  0.8 (YGLY 7122) X074822 55.77 24.44 19.79 1.8 17.28 ND ND 0.71 (YGLY 7122) α1,2 Mannosidase X074824 55.56 21.47 22.97 0.33 2.98 11.85  6.59 1.22 (YGLY 7118) X074824 54.68 21.67 23.65 0.4 22.5 ND ND 0.75 (YGLY 7118) α1,2 Mannosidase G2—Gal₂GlcNAc₂Man₃GlcNAc₂ N-glycans M6-M8—Man₆GlcNAc₂ to Man₈GlcNAc₂ N-glycans M9—Man₉GlcNAc₂ N-glycans M9+—Man₉GlcNAc₂ and larger N-glycans Hyb—hybrid N-glycans

Strains YGLY7115, 7117, and 7120 were cultivated in 3 L fermentors and processed through Blue SEPHAROSE 6 FF chromatography followed by hydroxyapatite (HA) chromatography. Aliquots from both the Blue pools and the HA pools were reduced and analyzed by 4-20% SDS-PAGE. Corresponding pools for YGLY3159 were included as positive controls. Corresponding pools for YGLY7395 were included as negative controls. FIG. 39A shows a Commassie blue stained 4-20% SDS-PAGE showing that both the Blue pools (left half of gel) and HA pools (right half of gel) produced rhEPO. FIG. 39B shows a Western blot of the same samples probed with anti-HCA antibodies. None of the tested strains had any detectable cross-binding activity to anti-HCA antibodies in either the Blue pool or the HA pool 1.

These results also show that deleting or disrupting all four BMT genes can result in strains that do not produce detectable cross-binding activity to anti-HCA antibodies in either the rhEPO after the preliminary Blue SEPHAROSE 6 FF capture step or the intermediate hydroxyapatite step using Type I 40 μM hydroxyapatite. These strains minimize the risk that rhEPO preparations will be made that contain cross-binding activity to anti-HCA antibodies. This enables the production of rhEPO with less risk of inducing an adverse immune response in the individual receiving the rhEPO.

Example 11

The blue pools containing rhEPO produced by YGLY7117 were further subjected to hydroxyapatite column chromatography and the rhEPO in the HA pools were analyzed for sialylation content. FIG. 40A and FIG. 40B show HPLC traces of the N-glycans from rhEPO produced in YGLY3159 compared to the N-glycans from rhEPO produced in YGLY7117, respectively. The figures also show that the hydroxyapatite column removed additional contaminants; thus, in this analysis the sialylation content of the rhEPO produced by YGLY7117 was about 99% (neutral N-glycans were about 1%) of which about 89% was A2 or bisialylated and about 10% was A1 or monosialylated.

Sialylation analysis of rhEPO produced in YGLY7117 following PEGylation according to the process in Example 3 was similar to the amount of sialylation prior to PEGylation; however, the amount of sialylation can vary to a limited extent depending for example, on what modifications were made to the growing conditions, e.g., medium compositions, feeding rate, etc (See Table 11). Thus, the methods herein produce rhEPO compositions having at least about 75% A2 sialylation or between about 75 and 89% A2 sialylation. Thus, the total sialic acid content is at least 4.5 moles sialic acid per mole of rhEPO, more specifically, from about 4.6 to 5.7 mole of sialic acid per mole of rhEPO.

TABLE 11 BPP FPP Avecia Avecia (2000 L) (800 L) (15 L) (100 L) (n = 3) (n = 2) (n = 2) (n = 1) Purity by SDS 99.5 ± 0.4% 99.4 ± 0.0% 99.4 ± 0.1% 99.4% PAGE (EPO related) (≧95.0%) Integrity by SDS 96.8 ± 0.7% 96.0 ± 2.2% 95.2 ± 2.0% 97.7% PAGE (Mono-PEG) (≧80.0%) Total sialic acid 5.0-5.7  4.6-4.7  5.1-5.2  5.2 (≧4.5 mol SA/mol protein) N- Linked glycan by 75.2-80.2% 74.2-77.8% 80.9-88.7% 83.9% CE (70-85% A2) A2—bi-sialylated CE—capillary electrophoresis SA—sialic acid BPP—Biologics Pilot Plant FPP—Fermentation Pilot Plant

A comparison of the pharmacokinetics of the rhEPO produced in the YGLY7117 produced in Example 3 with all four BMT genes disrupted or deleted and PEGylated was compared to PEGylated rhEPO produced from strain YGLY3159. The comparison showed that the PEGylated rhEPO produced in strain YGLY7117 had in vivo half-life and in vivo potency similar to that of YGLY3159 and ARANESP (See Tables 12 and 13).

TABLE 12 PK of rhEPO from YGLY3159 (CBA) vs YGLY7117 (no CBA) YGLY3159 YGLY7117 T½ (hr) 20.9 ± 2 20.6 ± 4 CBA—cross-binding activity

TABLE 13 Relative Potency 95% rhEPO source (Reticulocyte Production) Confidence Interval YGLY3159 vs 0.94 (0.77, 1.14) YGLY7117

Sequences

Sequences that were used to produce some of the strains disclosed in Examples 1-11 are provided in Table 14.

TABLE 14 SEQ ID NO: Description Sequence 1 S. cerevisiae AGGCCTCGCAACAACCTATAATTGAGTTAAGTGCCTTTCCAAGCT invertase AAAAAGTTTGAGGTTATAGGGGCTTAGCATCCACACGTCACAAT gene CTCGGGTATCGAGTATAGTATGTAGAATTACGGCAGGAGGTTTC (ScSUC2) CCAATGAACAAAGGACAGGGGCACGGTGAGCTGTCGAAGGTATC CATTTTATCATGTTTCGTTTGTACAAGCACGACATACTAAGACAT TTACCGTATGGGAGTTGTTGTCCTAGCGTAGTTCTCGCTCCCCCA GCAAAGCTCAAAAAAGTACGTCATTTAGAATAGTTTGTGAGCAA ATTACCAGTCGGTATGCTACGTTAGAAAGGCCCACAGTATTCTTC TACCAAAGGCGTGCCTTTGTTGAACTCGATCCATTATGAGGGCTT CCATTATTCCCCGCATTTTTATTACTCTGAACAGGAATAAAAAGA AAAAACCCAGTTTAGGAAATTATCCGGGGGCGAAGAAATACGCG TAGCGTTAATCGACCCCACGTCCAGGGTTTTTCCATGGAGGTTTC TGGAAAAACTGACGAGGAATGTGATTATAAATCCCTTTATGTGA TGTCTAAGACTTTTAAGGTACGCCCGATGTTTGCCTATTACCATC ATAGAGACGTTTCTTTTCGAGGAATGCTTAAACGACTTTGTTTGA CAAAAATGTTGCCTAAGGGCTCTATAGTAAACCATTTGGAAGAA AGATTTGACGACTTTTTTTTTTTGGATTTCGATCCTATAATCCTTC CTCCTGAAAAGAAACATATAAATAGATATGTATTATTCTTCAAAA CATTCTCTTGTTCTTGTGCTTTTTTTTTACCATATATCTTACTTTTT TTTTTCTCTCAGAGAAACAAGCAAAACAAAAAGCTTTTCTTTTCA CTAACGTATATG ATGCTTTTGCAAGCTTTCCTTTTCCTTTTGGCTG GTTTTGCAGCCAAAATATCTGCATCAATGACAAACGAAACTAGC GATAGACCTTTGGTCCACTTCACACCCAACAAGGGCTGGATGAA TGACCCAAATGGGTTGTGGTACGATGAAAAAGATGCCAAATGGC ATCTGTACTTTCAATACAACCCAAATGACACCGTATGGGGTACGC CATTGTTTTGGGGCCATGCTACTTCCGATGATTTGACTAATTGGG AAGATCAACCCATTGCTATCGCTCCCAAGCGTAACGATTCAGGT GCTTTCTCTGGCTCCATGGTGGTTGATTACAACAACACGAGTGGG TTTTTCAATGATACTATTGATCCAAGACAAAGATGCGTTGCGATT TGGACTTATAACACTCCTGAAAGTGAAGAGCAATACATTAGCTA TTCTCTTGATGGTGGTTACACTTTTACTGAATACCAAAAGAACCC TGTTTTAGCTGCCAACTCCACTCAATTCAGAGATCCAAAGGTGTT CTGGTATGAACCTTCTCAAAAATGGATTATGACGGCTGCCAAATC ACAAGACTACAAAATTGAAATTTACTCCTCTGATGACTTGAAGTC CTGGAAGCTAGAATCTGCATTTGCCAATGAAGGTTTCTTAGGCTA CCAATACGAATGTCCAGGTTTGATTGAAGTCCCAACTGAGCAAG ATCCTTCCAAATCTTATTGGGTCATGTTTATTTCTATCAACCCAGG TGCACCTGCTGGCGGTTCCTTCAACCAATATTTTGTTGGATCCTTC AATGGTACTCATTTTGAAGCGTTTGACAATCAATCTAGAGTGGTA GATTTTGGTAAGGACTACTATGCCTTGCAAACTTTCTTCAACACT GACCCAACCTACGGTTCAGCATTAGGTATTGCCTGGGCTTCAAAC TGGGAGTACAGTGCCTTTGTCCCAACTAACCCATGGAGATCATCC ATGTCTTTGGTCCGCAAGTTTTCTTTGAACACTGAATATCAAGCT AATCCAGAGACTGAATTGATCAATTTGAAAGCCGAACCAATATT GAACATTAGTAATGCTGGTCCCTGGTCTCGTTTTGCTACTAACAC AACTCTAACTAAGGCCAATTCTTACAATGTCGATTTGAGCAACTC GACTGGTACCCTAGAGTTTGAGTTGGTTTACGCTGTTAACACCAC ACAAACCATATCCAAATCCGTCTTTGCCGACTTATCACTTTGGTT CAAGGGTTTAGAAGATCCTGAAGAATATTTGAGAATGGGTTTTG AAGTCAGTGCTTCTTCCTTCTTTTTGGACCGTGGTAACTCTAAGG TCAAGTTTGTCAAGGAGAACCCATATTTCACAAACAGAATGTCT GTCAACAACCAACCATTCAAGTCTGAGAACGACCTAAGTTACTA TAAAGTGTACGGCCTACTGGATCAAAACATCTTGGAATTGTACTT CAACGATGGAGATGTGGTTTCTACAAATACCTACTTCATGACCAC CGGTAACGCTCTAGGATCTGTGAACATGACCACTGGTGTCGATA ATTTGTTCTACATTGACAAGTTCCAAGTAAGGGAAGTAAAATAG AGGTTATAAAACTTATTGTCTTTTTTATTTTTTTCAAAAGCCATTC TAAAGGGCTTTAGCTAACGAGTGACGAATGTAAAACTTTATGAT TTCAAAGAATACCTCCAAACCATTGAAAATGTATTTTTATTTTTA TTTTCTCCCGACCCCAGTTACCTGGAATTTGTTCTTTATGTACTTT ATATAAGTATAATTCTCTTAAAAATTTTTACTACTTTGCAATAGA CATCATTTTTTCACGTAATAAACCCACAATCGTAATGTAGTTGCC TTACACTACTAGGATGGACCTTTTTGCCTTTATCTGTTTTGTTACT GACACAATGAAACCGGGTAAAGTATTAGTTATGTGAAAATTTAA AAGCATTAAGTAGAAGTATACCATATTGTAAAAAAAAAAAGCGT TGTCTTCTACGTAAAAGTGTTCTCAAAAAGAAGTAGTGAGGGAA ATGGATACCAAGCTATCTGTAACAGGAGCTAAAAAATCTCAGGG AAAAGCTTCTGGTTTGGGAAACGGTCGAC 2 S. cerevisiae MLLQAFLFLLAGFAAKISASMTNETSDRPLVHFTPNKGWMNDPNGL invertase WYDEKDAKWHLYFQYNPNDTVWGTPLFWGHATSDDLTNWEDQPI (ScSUC2) AIAPKRNDSGAFSGSMVVDYNNTSGFFNDTIDPRQRCVAIWTYNTP ESEEQYISYSLDGGYTFTEYQKNPVLAANSTQFRDPKVFWYEPSQK WIMTAAKSQDYKIEIYSSDDLKSWKLESAFANEGFLGYQYECPGLIE VPTEQDPSKSYWVMFISINPGAPAGGSFNQYFVGSFNGTHFEAFDNQ SRVVDFGKDYYALQTFFNTDPTYGSALGIAWASNWEYSAFVPTNP WRSSMSLVRKFSLNTEYQANPETELINLKAEPILNISNAGPWSRFAT NTTLTKANSYNVDLSNSTGTLEFELVYAVNTTQTISKSVFADLSLWF KGLEDPEEYLRMGFEVSASSFFLDRGNSKVKFVKENPYFTNRMSVN NQPFKSENDLSYYKVYGLLDQNILELYFNDGDVVSTNTYFMTTGNA LGSVNMTTGVDNLFYIDKFQVREVK 3 K. lactis AAACGTAACGCCTGGCACTCTATTTTCTCAAACTTCTGGGACGGA UDP- AGAGCTAAATATTGTGTTGCTTGAACAAACCCAAAAAAACAAAA GlcNAc AAATGAACAAACTAAAACTACACCTAAATAAACCGTGTGTAAAA transporter CGTAGTACCATATTACTAGAAAAGATCACAAGTGTATCACACAT gene GTGCATCTCATATTACATCTTTTATCCAATCCATTCTCTCTATCCC (KIMNN2- GTCTGTTCCTGTCAGATTCTTTTTCCATAAAAAGAAGAAGACCCC 2) GAATCTCACCGGTACAATGCAAAACTGCTGAAAAAAAAAGAAA GTTCACTGGATACGGGAACAGTGCCAGTAGGCTTCACCACATGG ACAAAACAATTGACGATAAAATAAGCAGGTGAGCTTCTTTTTCA AGTCACGATCCCTTTATGTCTCAGAAACAATATATACAAGCTAAA CCCTTTTGAACCAGTTCTCTCTTCATAGTTATGTTCACATAAATTG CGGGAACAAGACTCCGCTGGCTGTCAGGTACACGTTGTAACGTT TTCGTCCGCCCAATTATTAGCACAACATTGGCAAAAAGAAAAAC TGCTCGTTTTCTCTACAGGTAAATTACAATTTTTTTCAGTAATTTT CGCTGAAAAATTTAAAGGGCAGGAAAAAAAGACGATCTCGACTT TGCATAGATGCAAGAACTGTGGTCAAAACTTGAAATAGTAATTT TGCTGTGCGTGAACTAATAAATATATATATATATATATATATATA TTTGTGTATTTTGTATATGTAATTGTGCACGTCTTGGCTATTGGAT ATAAGATTTTCGCGGGTTGATGACATAGAGCGTGTACTACTGTAA TAGTTGTATATTCAAAAGCTGCTGCGTGGAGAAAGACTAAAATA GATAAAAAGCACACATTTTGACTTCGGTACCGTCAACTTAGTGG GACAGTCTTTTATATTTGGTGTAAGCTCATTTCTGGTACTATTCGA AACAGAACAGTGTTTTCTGTATTACCGTCCAATCGTTTGTCATGA GTTTTGTATTGATTTTGTCGTTAGTGTTCGGAGGATGTTGTTCCAA TGTGATTAGTTTCGAGCACATGGTGCAAGGCAGCAATATAAATTT GGGAAATATTGTTACATTCACTCAATTCGTGTCTGTGACGCTAAT TCAGTTGCCCAATGCTTTGGACTTCTCTCACTTTCCGTTTAGGTTG CGACCTAGACACATTCCTCTTAAGATCCATATGTTAGCTGTGTTT TTGTTCTTTACCAGTTCAGTCGCCAATAACAGTGTGTTTAAATTT GACATTTCCGTTCCGATTCATATTATCATTAGATTTTCAGGTACC ACTTTGACGATGATAATAGGTTGGGCTGTTTGTAATAAGAGGTAC TCCAAACTTCAGGTGCAATCTGCCATCATTATGACGCTTGGTGCG ATTGTCGCATCATTATACCGTGACAAAGAATTTTCAATGGACAGT TTAAAGTTGAATACGGATTCAGTGGGTATGACCCAAAAATCTAT GTTTGGTATCTTTGTTGTGCTAGTGGCCACTGCCTTGATGTCATTG TTGTCGTTGCTCAACGAATGGACGTATAACAAGTACGGGAAACA TTGGAAAGAAACTTTGTTCTATTCGCATTTCTTGGCTCTACCGTTG TTTATGTTGGGGTACACAAGGCTCAGAGACGAATTCAGAGACCT CTTAATTTCCTCAGACTCAATGGATATTCCTATTGTTAAATTACC AATTGCTACGAAACTTTTCATGCTAATAGCAAATAACGTGACCCA GTTCATTTGTATCAAAGGTGTTAACATGCTAGCTAGTAACACGGA TGCTTTGACACTTTCTGTCGTGCTTCTAGTGCGTAAATTTGTTAGT CTTTTACTCAGTGTCTACATCTACAAGAACGTCCTATCCGTGACT GCATACCTAGGGACCATCACCGTGTTCCTGGGAGCTGGTTTGTAT TCATATGGTTCGGTCAAAACTGCACTGCCTCGCTGAAACAATCC ACGTCTGTATGATACTCGTTTCAGAATTTTTTTGATTTTCTGCCGG ATATGGTTTCTCATCTTTACAATCGCATTCTTAATTATACCAGAA CGTAATTCAATGATCCCAGTGACTCGTAACTCTTATATGTCAATT TAAGC 4 K. lactis MSFVLILSLVFGGCCSNVISFEHMVQGSNINLGNIVTFTQFVSVTLIQ UDP- LPNALDFSHFPFRLRPRHIPLKIHMLAVFLFFTSSVANNSVFKFDISVP GlcNAc IHIIIRFSGTTLTMIIGWAVCNKRYSKLQVQSAIIMTLGAIVASLYRDK transporter EFSMDSLKLNTDSVGMTQKSMFGIFVVLVATALMSLLSLLNEWTY (KIMNN2- NKYGKHWKETLFYSHFLALPLFMLGYTRLRDEFRDLLISSDSMDIPI 2) VKLPIATKLFMLIANNVTQFICIKGVNMLASNTDALTLSVVLLVRKF VSLLLSVYIYKNVLSVTAYLGTITVFLGAGLYSYGSVKTALPR 5 DNA ATGCTGCTTACCAAAAGGTTTTCAAAGCTGTTCAAGCTGACGTTC encodes ATAGTTTTGATATTGTGCGGGCTGTTCGTCATTACAAACAAATAC Mnn2 ATGGATGAGAACACGTCG leader (53) 6 Mnn2 MLLTKRFSKLFKLTFIVLILCGLFVITNKYMDENTS leader (53) 7 DNA ATGCTGCTTACCAAAAGGTTTTCAAAGCTGTTCAAGCTGACGTTC encodes ATAGTTTTGATATTGTGCGGGCTGTTCGTCATTACAAACAAATAC Mnn2 ATGGATGAGAACACGTCGGTCAAGGAGTACAAGGAGTACTTAGA leader (54) CAGATATGTCCAGAGTTACTCCAATAAGTATTCATCTTCCTCAGA The last 9 CGCCGCCAGCGCTGACGATTCAACCCCATTGAGGGACAATGATG nucleotides AGGCAGGCAATGAAAAGTTGAAAAGCTTCTACAACAACGTTTTC are the AACTTTCTAATGGTTGATTCGCCCGGGCGCGCC linker containing the AscI restriction site) 8 Mnn2 MLLTKRFSKLFKLTFIVLILCGLFVITNKYMDENTSVKEYKEYLDRY leader (54) VQSYSNKYSSSSD AASADDSTPLRDNDEAGNEKLKSFYNNVFNFLMVDSPGRA 9 DNA ATG AGA TTC CCA TCC ATC TTC ACT GCT GTT TTG TTC GCT encodes S. cerevisiae GCT TCT TCT GCT TTG GCT Mating Factor pre signal sequence 10 S. cerevisiae MRFPSIFTAVLFAASSALA Mating Factor pre signal sequence 11 DNA ATGCCCAGAAAAATATTTAACTACTTCATTTTGACTGTATTCATG encodes Pp GCAATTCTTGCTATTGTTTTACAATGGTCTATAGAGAATGGACAT SEC12 GGGCGCGCC (10) The last 9 nucleotides are the linker containing the AscI restriction site used for fusion to proteins of interest. 12 Pp SEC12 MPRKIFNYFILTVFMAILAIVLQWSIENGHGRA (10) 13 DNA ATGGCCCTCTTTCTCAGTAAGAGACTGTTGAGATTTACCGTCATT encodes GCAGGTGCGGTTATTGTTCTCCTCCTAACATTGAATTCCAACAGT ScMnt1 AGAACTCAGCAATATATTCCGAGTTCCATCTCCGCTGCATTTGAT (Kre2) (33) TTTACCTCAGGATCTATATCCCCTGAACAACAAGTCATCGGGCGC GCC 14 ScMnt1 MALFLSKRLLRFTVIAGAVIVLLLTLNSNSRTQQYIPSSISAAFDFTSG (Kre2) (33) SISPEQQVIGRA 15 DNA ATGAACACTATCCACATAATAAAATTACCGCTTAACTACGCCAA encodes CTACACCTCAATGAAACAAAAAATCTCTAAATTTTTCACCAACTT ScSEC12 CATCCTTATTGTGCTGCTTTCTTACATTTTACAGTTCTCCTATAAG (8) CACAATTTGCATTCCATGCTTTTCAATTACGCGAAGGACAATTTT The last 9 CTAACGAAAAGAGACACCATCTCTTCGCCCTACGTAGTTGATGA nucleotides AGACTTACATCAAACAACTTTGTTTGGCAACCACGGTACAAAAA are the CATCTGTACCTAGCGTAGATTCCATAAAAGTGCATGGCGTGGGG linker CGCGCC containing the AscI restriction site used for fusion to proteins of interest 16 ScSEC12 MNTIHIIKLPLNYANYTSMKQKISKFFTNFILIVLLSYILQFSYKHNLH (8) SMLFNYAKDNFLTKRDTISSPYVVDEDLHQTTLFGNHGTKTSVPSV DSIKVHGVGRA 17 DNA ATGTCTGCCAACCTAAAATATCTTTCCTTGGGAATTTTGGTGTTTC encodes AGACTACCAGTCTGGTTCTAACGATGCGGTATTCTAGGACTTTAA MmSLC35 AAGAGGAGGGGCCTCGTTATCTGTCTTCTACAGCAGTGGTTGTGG A3 UDP- CTGAATTTTTGAAGATAATGGCCTGCATCTTTTTAGTCTACAAAG GlcNAc ACAGTAAGTGTAGTGTGAGAGCACTGAATAGAGTACTGCATGAT transporter GAAATTCTTAATAAGCCCATGGAAACCCTGAAGCTCGCTATCCC GTCAGGGATATATACTCTTCAGAACAACTTACTCTATGTGGCACT GTCAAACCTAGATGCAGCCACTTACCAGGTTACATATCAGTTGA AAATACTTACAACAGCATTATTTTCTGTGTCTATGCTTGGTAAAA AATTAGGTGTGTACCAGTGGCTCTCCCTAGTAATTCTGATGGCAG GAGTTGCTTTTGTACAGTGGCCTTCAGATTCTCAAGAGCTGAACT CTAAGGACCTTTCAACAGGCTCACAGTTTGTAGGCCTCATGGCAG TTCTCACAGCCTGTTTTTCAAGTGGCTTTGCTGGAGTTTATTTTGA GAAAATCTTAAAAGAAACAAAACAGTCAGTATGGATAAGGAAC ATTCAACTTGGTTTCTTTGGAAGTATATTTGGATTAATGGGTGTA TACGTTTATGATGGAGAATTGGTCTCAAAGAATGGATTTTTTCAG GGATATAATCAACTGACGTGGATAGTTGTTGCTCTGCAGGCACTT GGAGGCCTTGTAATAGCTGCTGTCATCAAATATGCAGATAACATT TTAAAAGGATTTGCGACCTCCTTATCCATAATATTGTCAACAATA ATATCTTATTTTTGGTTGCAAGATTTTGTGCCAACCAGTGTCTTTT TCCTTGGAGCCATCCTTGTAATAGCAGCTACTTTCTTGTATGGTT ACGATCCCAAACCTGCAGGAAATCCCACTAAAGCATAG 18 MmSLC35 MSANLKYLSLGILVFQTTSLVLTMRYSRTLKEEGPRYLSSTAVVVAE A3 UDP- FLKIMACIFLVYKDSKCSVRALNRVLHDEILNKPMETLKLAIPSGIYT GlcNAc LQNNLLYVALSNLDAATYQVTYQLKILTTALFSVSMLGKKLGVYQ transporter WLSLVILMAGVAFVQWPSDSQELNSKDLSTGSQFVGLMAVLTACFS SGFAGVYFEKILKETKQSVWIRNIQLGFFGSIFGLMGVYVYDGELVS KNGFFQGYNQLTWIVVALQALGGLVIAAVIKYADNILKGFATSLSII LSTIISYFWLQDFVPTSVFFLGAILVIAATFLYGYDPKPAGNPTKA 19 DNA ATGAATAGCATACACATGAACGCCAATACGCTGAAGTACATCAG encodes CCTGCTGACGCTGACCCTGCAGAATGCCATCCTGGGCCTCAGCAT DmUGT GCGCTACGCCCGCACCCGGCCAGGCGACATCTTCCTCAGCTCCAC GGCCGTACTCATGGCAGAGTTCGCCAAACTGATCACGTGCCTGTT CCTGGTCTTCAACGAGGAGGGCAAGGATGCCCAGAAGTTTGTAC GCTCGCTGCACAAGACCATCATTGCGAATCCCATGGACACGCTG AAGGTGTGCGTCCCCTCGCTGGTCTATATCGTTCAAAACAATCTG CTGTACGTCTCTGCCTCCCATTTGGATGCGGCCACCTACCAGGTG ACGTACCAGCTGAAGATTCTCACCACGGCCATGTTCGCGGTTGTC ATTCTGCGCCGCAAGCTGCTGAACACGCAGTGGGGTGCGCTGCT GCTCCTGGTGATGGGCATCGTCCTGGTGCAGTTGGCCCAAACGG AGGGTCCGACGAGTGGCTCAGCCGGTGGTGCCGCAGCTGCAGCC ACGGCCGCCTCCTCTGGCGGTGCTCCCGAGCAGAACAGGATGCT CGGACTGTGGGCCGCACTGGGCGCCTGCTTCCTCTCCGGATTCGC GGGCATCTACTTTGAGAAGATCCTCAAGGGTGCCGAGATCTCCG TGTGGATGCGGAATGTGCAGTTGAGTCTGCTCAGCATTCCCTTCG GCCTGCTCACCTGTTTCGTTAACGACGGCAGTAGGATCTTCGACC AGGGATTCTTCAAGGGCTACGATCTGTTTGTCTGGTACCTGGTCC TGCTGCAGGCCGGCGGTGGATTGATCGTTGCCGTGGTGGTCAAG TACGCGGATAACATTCTCAAGGGCTTCGCCACCTCGCTGGCCATC ATCATCTCGTGCGTGGCCTCCATATACATCTTCGACTTCAATCTC ACGCTGCAGTTCAGCTTCGGAGCTGGCCTGGTCATCGCCTCCATA TTTCTCTACGGCTACGATCCGGCCAGGTCGGCGCCGAAGCCAACT ATGCATGGTCCTGGCGGCGATGAGGAGAAGCTGCTGCCGCGCGT CTAG 20 DmUGT MNSIHMNANTLKYISLLTLTLQNAILGLSMRYARTRPGDIFLSSTAV LMAEFAKLITCLFLVFNEEGKDAQKFVRSLHKTIIANPMDTLKVCVP SLVYIVQNNLLYVSASHLDAATYQVTYQLKILTTAMFAVVILRRKL LNTQWGALLLLVMGIVLVQLAQTEGPTSGSAGGAAAAATAASSGG APEQNRMLGLWAALGACFLSGFAGIYFEKILKGAEISVWMRNVQLS LLSIPFGLLTCFVNDGSRIFDQGFFKGYDLFVWYLVLLQAGGGLIVA VVVKYADNILKGFATSLAIIISCVASIYIFDFNLTLQFSFGAGLVIASIF LYGYDPARSAPKPTMHGPGGDEEKLLPRV 21 DNA ATGACAGCTCAGTTACAAAGTGAAAGTACTTCTAAAATTGTTTTG encodes GTTACAGGTGGTGCTGGATACATTGGTTCACACACTGTGGTAGA ScGAL10 GCTAATTGAGAATGGATATGACTGTGTTGTTGCTGATAACCTGTC GAATTCAACTTATGATTCTGTAGCCAGGTTAGAGGTCTTGACCAA GCATCACATTCCCTTCTATGAGGTTGATTTGTGTGACCGAAAAGG TCTGGAAAAGGTTTTCAAAGAATATAAAATTGATTCGGTAATTCA CTTTGCTGGTTTAAAGGCTGTAGGTGAATCTACACAAATCCCGCT GAGATACTATCACAATAACATTTTGGGAACTGTCGTTTTATTAGA GTTAATGCAACAATACAACGTTTCCAAATTTGTTTTTTCATCTTCT GCTACTGTCTATGGTGATGCTACGAGATTCCCAAATATGATTCCT ATCCCAGAAGAATGTCCCTTAGGGCCTACTAATCCGTATGGTCAT ACGAAATACGCCATTGAGAATATCTTGAATGATCTTTACAATAGC GACAAAAAAAGTTGGAAGTTTGCTATCTTGCGTTATTTTAACCCA ATTGGCGCACATCCCTCTGGATTAATCGGAGAAGATCCGCTAGG TATACCAAACAATTTGTTGCCATATATGGCTCAAGTAGCTGTTGG TAGGCGCGAGAAGCTTTACATCTTCGGAGACGATTATGATTCCA GAGATGGTACCCCGATCAGGGATTATATCCACGTAGTTGATCTA GCAAAAGGTCATATTGCAGCCCTGCAATACCTAGAGGCCTACAA TGAAAATGAAGGTTTGTGTCGTGAGTGGAACTTGGGTTCCGGTA AAGGTTCTACAGTTTTTGAAGTTTATCATGCATTCTGCAAAGCTT CTGGTATTGATCTTCCATACAAAGTTACGGGCAGAAGAGCAGGT GATGTTTTGAACTTGACGGCTAAACCAGATAGGGCCAAACGCGA ACTGAAATGGCAGACCGAGTTGCAGGTTGAAGACTCCTGCAAGG ATTTATGGAAATGGACTACTGAGAATCCTTTTGGTTACCAGTTAA GGGGTGTCGAGGCCAGATTTTCCGCTGAAGATATGCGTTATGAC GCAAGATTTGTGACTATTGGTGCCGGCACCAGATTTCAAGCCAC GTTTGCCAATTTGGGCGCCAGCATTGTTGACCTGAAAGTGAACG GACAATCAGTTGTTCTTGGCTATGAAAATGAGGAAGGGTATTTG AATCCTGATAGTGCTTATATAGGCGCCACGATCGGCAGGTATGCT AATCGTATTTCGAAGGGTAAGTTTAGTTTATGCAACAAAGACTAT CAGTTAACCGTTAATAACGGCGTTAATGCGAATCATAGTAGTATC GGTTCTTTCCACAGAAAAAGATTTTTGGGACCCATCATTCAAAAT CCTTCAAAGGATGTTTTTACCGCCGAGTACATGCTGATAGATAAT GAGAAGGACACCGAATTTCCAGGTGATCTATTGGTAACCATACA GTATACTGTGAACGTTGCCCAAAAAAGTTTGGAAATGGTATATA AAGGTAAATTGACTGCTGGTGAAGCGACGCCAATAAATTTAACA AATCATAGTTATTTCAATCTGAACAAGCCATATGGAGACACTATT GAGGGTACGGAGATTATGGTGCGTTCAAAAAAATCTGTTGATGT CGACAAAAACATGATTCCTACGGGTAATATCGTCGATAGAGAAA TTGCTACCTTTAACTCTACAAAGCCAACGGTCTTAGGCCCCAAAA ATCCCCAGTTTGATTGTTGTTTTGTGGTGGATGAAAATGCTAAGC CAAGTCAAATCAATACTCTAAACAATGAATTGACGCTTATTGTCA AGGCTTTTCATCCCGATTCCAATATTACATTAGAAGTTTTAAGTA CAGAGCCAACTTATCAATTTTATACCGGTGATTTCTTGTCTGCTG GTTACGAAGCAAGACAAGGTTTTGCAATTGAGCCTGGTAGATAC ATTGATGCTATCAATCAAGAGAACTGGAAAGATTGTGTAACCTT GAAAAACGGTGAAACTTACGGGTCCAAGATTGTCTACAGATTTT CCTGA 22 ScGal10 MTAQLQSESTSKIVLVTGGAGYIGSHTVVELIENGYDCVVADNLSN STYDSVARLEVLTKHHIPFYEVDLCDRKGLEKVFKEYKIDSVIHFAG LKAVGESTQIPLRYYHNNILGTVVLLELMQQYNVSKFVFSSSATVY GDATRFPNMIPIPEECPLGPTNPYGHTKYAIENILNDLYNSDKKSWK FAILRYFNPIGAHPSGLIGEDPLGIPNNLLPYMAQVAVGRREKLYIFG DDYDSRDGTPIRDYIHVVDLAKGHIAALQYLEAYNENEGLCREWNL GSGKGSTVFEVYHAFCKASGIDLPYKVTGRRAGDVLNLTAKPDRA KRELKWQTELQVEDSCKDLWKWTTENPFGYQLRGVEARFSAEDM RYDARFVTIGAGTRFQATFANLG ASIVDLKVNGQSVVLGYENEEGYLNPDSAYIGATIGRYANRISKGKF SLCNKDYQLTVNNGVNANHSSIGSFHRKRFLGPIIQNPSKDVFTAEY MLIDNEKDTEFPGDLLVTIQYTVNVAQKSLEMVYKGKLTAGEATPI NLTNHSYFNLNKPYGDTIEGTEIMVRSKKSVDVDKNMIPTGNIVDRE IATFNSTKPTVLGPKNPQFDCCFVVDENAKPSQINTLNNELTLIVKAF HPDSNITLEVLSTEPTYQFYTGDFLSAGYEARQGFAIEPGRYIDAINQ ENWKDCVTLKNGETYGSKIVYRFS 23 hGalT GGTAGAGATTTGTCTAGATTGCCACAGTTGGTTGGTGTTTCCACT codon CCATTGCAAGGAGGTTCTAACTCTGCTGCTGCTATTGGTCAATCT optimized TCCGGTGAGTTGAGAACTGGTGGAGCTAGACCACCTCCACCATT (XB) GGGAGCTTCCTCTCAACCAAGACCAGGTGGTGATTCTTCTCCAGT TGTTGACTCTGGTCCAGGTCCAGCTTCTAACTTGACTTCCGTTCC AGTTCCACACACTACTGCTTTGTCCTTGCCAGCTTGTCCAGAAGA ATCCCCATTGTTGGTTGGTCCAATGTTGATCGAGTTCAACATGCC AGTTGACTTGGAGTTGGTTGCTAAGCAGAACCCAAACGTTAAGA TGGGTGGTAGATACGCTCCAAGAGACTGTGTTTCCCCACACAAA GTTGCTATCATCATCCCATTCAGAAACAGACAGGAGCACTTGAA GTACTGGTTGTACTACTTGCACCCAGTTTTGCAAAGACAGCAGTT GGACTACGGTATCTACGTTATCAACCAGGCTGGTGACACTATTTT CAACAGAGCTAAGTTGTTGAATGTTGGTTTCCAGGAGGCTTTGAA GGATTACGACTACACTTGTTTCGTTTTCTCCGACGTTGACTTGATT CCAATGAACGACCACAACGCTTACAGATGTTTCTCCCAGCCAAG ACACATTTCTGTTGCTATGGACAAGTTCGGTTTCTCCTTGCCATA CGTTCAATACTTCGGTGGTGTTTCCGCTTTGTCCAAGCAGCAGTT CTTGACTATCAACGGTTTCCCAAACAATTACTGGGGATGGGGTG GTGAAGATGACGACATCTTTAACAGATTGGTTTTCAGAGGAATG TCCATCTCTAGACCAAACGCTGTTGTTGGTAGATGTAGAATGATC AGACACTCCAGAGACAAGAAGAACGAGCCAAACCCACAAAGAT TCGACAGAATCGCTCACACTAAGGAAACTATGTTGTCCGACGGA TTGAACTCCTTGACTTACCAGGTTTTGGACGTTCAGAGATACCCA TTGTACACTCAGATCACTGTTGACATCGGTACTCCATCCTAG 24 hGalT I GRDLSRLPQLVGVSTPLQGGSNSAAAIGQSSGELRTGGARPPPPLGA catalytic SSQPRPGGDSSPVVDSGPGPASNLTSVPVPHTTALSLPACPEESPLLV doman GPMLIEFNMPVDLELVAKQNPNVKMGGRYAPRDCVSPHKVAIIIPFR (XB) NRQEHLKYWLYYLHPVLQRQQLDYGIYVINQAGDTIFNRAKLLNV GFQEALKDYDYTCFVFSDVDLIPMNDHNAYRCFSQPRHISVAMDKF GFSLPYVQYFGGVSALSKQQFLTINGFPNNYWGWGGEDDDIFNRLV FRGMSISRPNAVVGRCRMIRHSRDKKNEPNPQRFDRIAHTKETMLS DGLNSLTYQVLDVQRYPLYTQITVDIGTPS 25 DNA TCAGTCAGTGCTCTTGATGGTGACCCAGCAAGTTTGACCAGAGA encodes AGTGATTAGATTGGCCCAAGACGCAGAGGTGGAGTTGGAGAGAC human AACGTGGACTGCTGCAGCAAATCGGAGATGCATTGTCTAGTCAA GnTI AGAGGTAGGGTGCCTACCGCAGCTCCTCCAGCACAGCCTAGAGT catalytic GCATGTGACCCCTGCACCAGCTGTGATTCCTATCTTGGTCATCGC doman CTGTGACAGATCTACTGTTAGAAGATGTCTGGACAAGCTGTTGCA (NA) TTACAGACCATCTGCTGAGTTGTTCCCTATCATCGTTAGTCAAGA Codon- CTGTGGTCACGAGGAGACTGCCCAAGCCATCGCCTCCTACGGAT optimized CTGCTGTCACTCACATCAGACAGCCTGACCTGTCATCTATTGCTG TGCCACCAGACCACAGAAAGTTCCAAGGTTACTACAAGATCGCT AGACACTACAGATGGGCATTGGGTCAAGTCTTCAGACAGTTTAG ATTCCCTGCTGCTGTGGTGGTGGAGGATGACTTGGAGGTGGCTCC TGACTTCTTTGAGTACTTTAGAGCAACCTATCCATTGCTGAAGGC AGACCCATCCCTGTGGTGTGTCTCTGCCTGGAATGACAACGGTAA GGAGCAAATGGTGGACGCTTCTAGGCCTGAGCTGTTGTACAGAA CCGACTTCTTTCCTGGTCTGGGATGGTTGCTGTTGGCTGAGTTGT GGGCTGAGTTGGAGCCTAAGTGGCCAAAGGCATTCTGGGACGAC TGGATGAGAAGACCTGAGCAAAGACAGGGTAGAGCCTGTATCAG ACCTGAGATCTCAAGAACCATGACCTTTGGTAGAAAGGGAGTGT CTCACGGTCAATTCTTTGACCAACACTTGAAGTTTATCAAGCTGA ACCAGCAATTTGTGCACTTCACCCAACTGGACCTGTCTTACTTGC AGAGAGAGGCCTATGACAGAGATTTCCTAGCTAGAGTCTACGGA GCTCCTCAACTGCAAGTGGAGAAAGTGAGGACCAATGACAGAAA GGAGTTGGGAGAGGTGAGAGTGCAGTACACTGGTAGGGACTCCT TTAAGGCTTTCGCTAAGGCTCTGGGTGTCATGGATGACCTTAAGT CTGGAGTTCCTAGAGCTGGTTACAGAGGTATTGTCACCTTTCAAT TCAGAGGTAGAAGAGTCCACTTGGCTCCTCCACCTACTTGGGAG GGTTATGATCCTTCTTGGAATTAG 26 Human SVSALDGDPASLTREVIRLAQDAEVELERQRGLLQQIGDALSSQRGR GnT I VPTAAPPAQPRVHVTPAPAVIPILVIACDRSTVRRCLDKLLHYRPSAE catalytic LFPIIVSQDCGHEETAQAIASYGSAVTHIRQPDLSSIAVPPDHRKFQG doman YYKIARHYRWALGQVFRQFRFPAAVVVEDDLEVAPDFFEYFRATYP (NA) LLKADPSLWCVSAWNDNGKEQMVDASRPELLYRTDFFPGLGWLLL AELWAELEPKWPKAFWDDWMRRPEQRQGRACIRPEISRTMTFGRK GVSHGQFFDQHLKFIKLNQQFVHFTQLDLSYLQREAYDRDFLARVY GAPQLQVEKVRTNDRKELGEVRVQYTGRDSFKAFAKALGVMDDL KSGVPRAGYRGIVTFQFRGRRVHLAPPPTWEGYDPSWN 27 DNA GAGCCCGCTGACGCCACCATCCGTGAGAAGAGGGCAAAGATCAA encodes AGAGATGATGACCCATGCTTGGAATAATTATAAACGCTATGCGT Mm ManI GGGGCTTGAACGAACTGAAACCTATATCAAAAGAAGGCCATTCA catalytic AGCAGTTTGTTTGGCAACATCAAAGGAGCTACAATAGTAGATGC doman CCTGGATACCCTTTTCATTATGGGCATGAAGACTGAATTTCAAGA (FB) AGCTAAATCGTGGATTAAAAAATATTTAGATTTTAATGTGAATGC TGAAGTTTCTGTTTTTGAAGTCAACATACGCTTCGTCGGTGGACT GCTGTCAGCCTACTATTTGTCCGGAGAGGAGATATTTCGAAAGA AAGCAGTGGAACTTGGGGTAAAATTGCTACCTGCATTTCATACTC CCTCTGGAATACCTTGGGCATTGCTGAATATGAAAAGTGGGATC GGGCGGAACTGGCCCTGGGCCTCTGGAGGCAGCAGTATCCTGGC CGAATTTGGAACTCTGCATTTAGAGTTTATGCACTTGTCCCACTT ATCAGGAGACCCAGTCTTTGCCGAAAAGGTTATGAAAATTCGAA CAGTGTTGAACAAACTGGACAAACCAGAAGGCCTTTATCCTAAC TATCTGAACCCCAGTAGTGGACAGTGGGGTCAACATCATGTGTC GGTTGGAGGACTTGGAGACAGCTTTTATGAATATTTGCTTAAGGC GTGGTTAATGTCTGACAAGACAGATCTCGAAGCCAAGAAGATGT ATTTTGATGCTGTTCAGGCCATCGAGACTCACTTGATCCGCAAGT CAAGTGGGGGACTAACGTACATCGCAGAGTGGAAGGGGGGCCTC CTGGAACACAAGATGGGCCACCTGACGTGCTTTGCAGGAGGCAT GTTTGCACTTGGGGCAGATGGAGCTCCGGAAGCCCGGGCCCAAC ACTACCTTGAACTCGGAGCTGAAATTGCCCGCACTTGTCATGAAT CTTATAATCGTACATATGTGAAGTTGGGACCGGAAGCGTTTCGAT TTGATGGCGGTGTGGAAGCTATTGCCACGAGGCAAAATGAAAAG TATTACATCTTACGGCCCGAGGTCATCGAGACATACATGTACATG TGGCGACTGACTCACGACCCCAAGTACAGGACCTGGGCCTGGGA AGCCGTGGAGGCTCTAGAAAGTCACTGCAGAGTGAACGGAGGCT ACTCAGGCTTACGGGATGTTTACATTGCCCGTGAGAGTTATGACG ATGTCCAGCAAAGTTTCTTCCTGGCAGAGACACTGAAGTATTTGT ACTTGATATTTTCCGATGATGACCTTCTTCCACTAGAACACTGGA TCTTCAACACCGAGGCTCATCCTTTCCCTATACTCCGTGAACAGA AGAAGGAAATTGATGGCAAAGAGAAATGA 28 Mm ManI EPADATIREKRAKIKEMMTHAWNNYKRYAWGLNELKPISKEGHSS catalytic SLFGNIKGATIVDALDTLFIMGMKTEFQEAKSWIKKYLDFNVNAEV doman SVFEVNIRFVGGLLSAYYLSGEEIFRKKAVELGVKLLPAFHTPSGIPW (FB) ALLNMKSGIGRNWPWASGGSSILAEFGTLHLEFMHLSHLSGDPVFA EKVMKIRTVLNKLDKPEGLYPNYLNPSSGQWGQHHVSVGGLGDSF YEYLLKAWLMSDKTDLEAKKMYFDAVQAIETHLIRKSSGGLTYIAE WKGGLLEHKMGHLTCFAGGMFALGADGAPEARAQHYLELGAEIA RTCHESYNRTYVKLGPEAFRFDGGVEAIATRQNEKYYILRPEVIETY MYMWRLTHDPKYRTWAWEAVEALESHCRVNGGYSGLRDVYIARE SYDDVQQSFFLAETLKYLYLIFSDDDLLPLEHWIFNTEAHPFPILREQ KKEIDGKEK 29 DNA CGCGCCGGATCTCCCAACCCTACGAGGGCGGCAGCAGTCAAGGC encodes Tr CGCATTCCAGACGTCGTGGAACGCTTACCACCATTTTGCCTTTCC ManI CCATGACGACCTCCACCCGGTCAGCAACAGCTTTGATGATGAGA catalytic GAAACGGCTGGGGCTCGTCGGCAATCGATGGCTTGGACACGGCT doman ATCCTCATGGGGGATGCCGACATTGTGAACACGATCCTTCAGTAT GTACCGCAGATCAACTTCACCACGACTGCGGTTGCCAACCAAGG CATCTCCGTGTTCGAGACCAACATTCGGTACCTCGGTGGCCTGCT TTCTGCCTATGACCTGTTGCGAGGTCCTTTCAGCTCCTTGGCGAC AAACCAGACCCTGGTAAACAGCCTTCTGAGGCAGGCTCAAACAC TGGCCAACGGCCTCAAGGTTGCGTTCACCACTCCCAGCGGTGTCC CGGACCCTACCGTCTTCTTCAACCCTACTGTCCGGAGAAGTGGTG CATCTAGCAACAACGTCGCTGAAATTGGAAGCCTGGTGCTCGAG TGGACACGGTTGAGCGACCTGACGGGAAACCCGCAGTATGCCCA GCTTGCGCAGAAGGGCGAGTCGTATCTCCTGAATCCAAAGGGAA GCCCGGAGGCATGGCCTGGCCTGATTGGAACGTTTGTCAGCACG AGCAACGGTACCTTTCAGGATAGCAGCGGCAGCTGGTCCGGCCT CATGGACAGCTTCTACGAGTACCTGATCAAGATGTACCTGTACG ACCCGGTTGCGTTTGCACACTACAAGGATCGCTGGGTCCTTGCTG CCGACTCGACCATTGCGCATCTCGCCTCTCACCCGTCGACGCGCA AGGACTTGACCTTTTTGTCTTCGTACAACGGACAGTCTACGTCGC CAAACTCAGGACATTTGGCCAGTTTTGCCGGTGGCAACTTCATCT TGGGAGGCATTCTCCTGAACGAGCAAAAGTACATTGACTTTGGA ATCAAGCTTGCCAGCTCGTACTTTGCCACGTACAACCAGACGGCT TCTGGAATCGGCCCCGAAGGCTTCGCGTGGGTGGACAGCGTGAC GGGCGCCGGCGGCTCGCCGCCCTCGTCCCAGTCCGGGTTCTACTC GTCGGCAGGATTCTGGGTGACGGCACCGTATTACATCCTGCGGC CGGAGACGCTGGAGAGCTTGTACTACGCATACCGCGTCACGGGC GACTCCAAGTGGCAGGACCTGGCGTGGGAAGCGTTCAGTGCCAT TGAGGACGCATGCCGCGCCGGCAGCGCGTACTCGTCCATCAACG ACGTGACGCAGGCCAACGGCGGGGGTGCCTCTGACGATATGGAG AGCTTCTGGTTTGCCGAGGCGCTCAAGTATGCGTACCTGATCTTT GCGGAGGAGTCGGATGTGCAGGTGCAGGCCAACGGCGGGAACA AATTTGTCTTTAACACGGAGGCGCACCCCTTTAGCATCCGTTCAT CATCACGACGGGGCGGCCACCTTGCTTAA 30 Tr Man I RAGSPNPTRAAAVKAAFQTSWNAYHHFAFPHDDLHPVSNSFDDER catalytic NGWGSSAIDGLDTAILMGDADIVNTILQYVPQINFTTTAVANQGISV doman FETNIRYLGGLLSAYDLLRGPFSSLATNQTLVNSLLRQAQTLANGLK VAFTTPSGVPDPTVFFNPTVRRSGASSNNVAEIGSLVLEWTRLSDLT GNPQYAQLAQKGESYLLNPKGSPEAWPGLIGTFVSTSNGTFQDSSGS WSGLMDSFYEYLIKMYLYDPVAFAHYKDRWVLAADSTIAHLASHP STRKDLTFLSSYNGQSTSPNSGHLASFAGGNFILGGILLNEQKYIDFG IKLASSYFATYNQTASGIGPEGFAWVDSVTGAGGSPPSSQSGFYSSA GFWVTAPYYILRPETLESLYYAYRVTGDSKWQDLAWEAFSAIEDAC RAGSAYSSINDVTQANGGGASDDMESFWFAEALKYAYLIFAEESDV QVQANGGNKFVFNTEAHPFSIRSSSRRGGHLA 31 DNA TCCTTGGTTTACCAATTGAACTTCGACCAGATGTTGAGAAACGTT encodes GACAAGGACGGTACTTGGTCTCCTGGTGAGTTGGTTTTGGTTGTT Rat GnT II CAGGTTCACAACAGACCAGAGTACTTGAGATTGTTGATCGACTC (TC) CTTGAGAAAGGCTCAAGGTATCAGAGAGGTTTTGGTTATCTTCTC Codon- CCACGATTTCTGGTCTGCTGAGATCAACTCCTTGATCTCCTCCGTT optimized GACTTCTGTCCAGTTTTGCAGGTTTTCTTCCCATTCTCCATCCAAT TGTACCCATCTGAGTTCCCAGGTTCTGATCCAAGAGACTGTCCAA GAGACTTGAAGAAGAACGCTGCTTTGAAGTTGGGTTGTATCAAC GCTGAATACCCAGATTCTTTCGGTCACTACAGAGAGGCTAAGTTC TCCCAAACTAAGCATCATTGGTGGTGGAAGTTGCACTTTGTTTGG GAGAGAGTTAAGGTTTTGCAGGACTACACTGGATTGATCTTGTTC TTGGAGGAGGATCATTACTTGGCTCCAGACTTCTACCACGTTTTC AAGAAGATGTGGAAGTTGAAGCAACAAGAGTGTCCAGGTTGTGA CGTTTTGTCCTTGGGAACTTACACTACTATCAGATCCTTCTACGG TATCGCTGACAAGGTTGACGTTAAGACTTGGAAGTCCACTGAAC ACAACATGGGATTGGCTTTGACTAGAGATGCTTACCAGAAGTTG ATCGAGTGTACTGACACTTTCTGTACTTACGACGACTACAACTGG GACTGGACTTTGCAGTACTTGACTTTGGCTTGTTTGCCAAAAGTT TGGAAGGTTTTGGTTCCACAGGCTCCAAGAATTTTCCACGCTGGT GACTGTGGAATGCACCACAAGAAAACTTGTAGACCATCCACTCA GTCCGCTCAAATTGAGTCCTTGTTGAACAACAACAAGCAGTACTT GTTCCCAGAGACTTTGGTTATCGGAGAGAAGTTTCCAATGGCTGC TATTTCCCCACCAAGAAAGAATGGTGGATGGGGTGATATTAGAG ACCACGAGTTGTGTAAATCCTACAGAAGATTGCAGTAG 32 Rat GnTII SLVYQLNFDQMLRNVDKDGTWSPGELVLVVQVHNRPEYLRLLIDS (TC) LRKAQGIREVLVIFSHDFWSAEINSLISSVDFCPVLQVFFPFSIQLYPS EFPGSDPRDCPRDLKKNAALKLGCINAEYPDSFGHYREAKFSQTKH HWWWKLHFVWERVKVLQDYTGLILFLEEDHYLAPDFYHVFKKMW KLKQQECPGCDVLSLGTYTTIRSFYGIADKVDVKTWKSTEHNMGLA LTRDAYQKLIECTDTFCTYDDYNWDWTLQYLTLACLPKVWKVLVP QAPRIFHAGDCGMHHKKTCRPSTQSAQIESLLNNNKQYLFPETLVIG EKFPMAAISPPRKNGGWGDIRDHELCKSYRRLQ 33 DNA AGAGACGATCCAATTAGACCTCCATTGAAGGTTGCTAGATCCCC encodes AAGACCAGGTCAATGTCAAGATGTTGTTCAGGACGTCCCAAACG Drosophila TTGATGTCCAGATGTTGGAGTTGTACGATAGAATGTCCTTCAAGG melanogaster ACATTGATGGTGGTGTTTGGAAGCAGGGTTGGAACATTAAGTAC ManII GATCCATTGAAGTACAACGCTCATCACAAGTTGAAGGTCTTCGTT codon- GTCCCACACTCCCACAACGATCCTGGTTGGATTCAGACCTTCGAG optimized GAATACTACCAGCACGACACCAAGCACATCTTGTCCAACGCTTT (KD) GAGACATTTGCACGACAACCCAGAGATGAAGTTCATCTGGGCTG AAATCTCCTACTTCGCTAGATTCTACCACGATTTGGGTGAGAACA AGAAGTTGCAGATGAAGTCCATCGTCAAGAACGGTCAGTTGGAA TTCGTCACTGGTGGATGGGTCATGCCAGACGAGGCTAACTCCCA CTGGAGAAACGTTTTGTTGCAGTTGACCGAAGGTCAAACTTGGTT GAAGCAATTCATGAACGTCACTCCAACTGCTTCCTGGGCTATCGA TCCATTCGGACACTCTCCAACTATGCCATACATTTTGCAGAAGTC TGGTTTCAAGAATATGTTGATCCAGAGAACCCACTACTCCGTTAA GAAGGAGTTGGCTCAACAGAGACAGTTGGAGTTCTTGTGGAGAC AGATCTGGGACAACAAAGGTGACACTGCTTTGTTCACCCACATG ATGCCATTCTACTCTTACGACATTCCTCATACCTGTGGTCCAGAT CCAAAGGTTTGTTGTCAGTTCGATTTCAAAAGAATGGGTTCCTTC GGTTTGTCTTGTCCATGGAAGGTTCCACCTAGAACTATCTCTGAT CAAAATGTTGCTGCTAGATCCGATTTGTTGGTTGATCAGTGGAAG AAGAAGGCTGAGTTGTACAGAACCAACGTCTTGTTGATTCCATTG GGTGACGACTTCAGATTCAAGCAGAACACCGAGTGGGATGTTCA GAGAGTCAACTACGAAAGATTGTTCGAACACATCAACTCTCAGG CTCACTTCAATGTCCAGGCTCAGTTCGGTACTTTGCAGGAATACT TCGATGCTGTTCACCAGGCTGAAAGAGCTGGACAAGCTGAGTTC CCAACCTTGTCTGGTGACTTCTTCACTTACGCTGATAGATCTGAT AACTACTGGTCTGGTTACTACACTTCCAGACCATACCATAAGAGA ATGGACAGAGTCTTGATGCACTACGTTAGAGCTGCTGAAATGTT GTCCGCTTGGCACTCCTGGGACGGTATGGCTAGAATCGAGGAAA GATTGGAGCAGGCTAGAAGAGAGTTGTCCTTGTTCCAGCACCAC GACGGTATTACTGGTACTGCTAAAACTCACGTTGTCGTCGACTAC GAGCAAAGAATGCAGGAAGCTTTGAAAGCTTGTCAAATGGTCAT GCAACAGTCTGTCTACAGATTGTTGACTAAGCCATCCATCTACTC TCCAGACTTCTCCTTCTCCTACTTCACTTTGGACGACTCCAGATG GCCAGGTTCTGGTGTTGAGGACTCTAGAACTACCATCATCTTGGG TGAGGATATCTTGCCATCCAAGCATGTTGTCATGCACAACACCTT GCCACACTGGAGAGAGCAGTTGGTTGACTTCTACGTCTCCTCTCC ATTCGTTTCTGTTACCGACTTGGCTAACAATCCAGTTGAGGCTCA GGTTTCTCCAGTTTGGTCTTGGCACCACGACACTTTGACTAAGAC TATCCACCCACAAGGTTCCACCACCAAGTACAGAATCATCTTCAA GGCTAGAGTTCCACCAATGGGTTTGGCTACCTACGTTTTGACCAT CTCCGATTCCAAGCCAGAGCACACCTCCTACGCTTCCAATTTGTT GCTTAGAAAGAACCCAACTTCCTTGCCATTGGGTCAATACCCAG AGGATGTCAAGTTCGGTGATCCAAGAGAGATCTCCTTGAGAGTT GGTAACGGTCCAACCTTGGCTTTCTCTGAGCAGGGTTTGTTGAAG TCCATTCAGTTGACTCAGGATTCTCCACATGTTCCAGTTCACTTC AAGTTCTTGAAGTACGGTGTTAGATCTCATGGTGATAGATCTGGT GCTTACTTGTTCTTGCCAAATGGTCCAGCTTCTCCAGTCGAGTTG GGTCAGCCAGTTGTCTTGGTCACTAAGGGTAAATTGGAGTCTTCC GTTTCTGTTGGTTTGCCATCTGTCGTTCACCAGACCATCATGAGA GGTGGTGCTCCAGAGATTAGAAATTTGGTCGATATTGGTTCTTTG GACAACACTGAGATCGTCATGAGATTGGAGACTCATATCGACTC TGGTGATATCTTCTACACTGATTTGAATGGATTGCAATTCATCAA GAGGAGAAGATTGGACAAGTTGCCATTGCAGGCTAACTACTACC CAATTCCATCTGGTATGTTCATTGAGGATGCTAATACCAGATTGA CTTTGTTGACCGGTCAACCATTGGGTGGATCTTCTTTGGCTTCTG GTGAGTTGGAGATTATGCAAGATAGAAGATTGGCTTCTGATGAT GAAAGAGGTTTGGGTCAGGGTGTTTTGGACAACAAGCCAGTTTT GCATATTTACAGATTGGTCTTGGAGAAGGTTAACAACTGTGTCAG ACCATCTAAGTTGCATCCAGCTGGTTACTTGACTTCTGCTGCTCA CAAAGCTTCTCAGTCTTTGTTGGATCCATTGGACAAGTTCATCTT CGCTGAAAATGAGTGGATCGGTGCTCAGGGTCAATTCGGTGGTG ATCATCCATCTGCTAGAGAGGATTTGGATGTCTCTGTCATGAGAA GATTGACCAAGTCTTCTGCTAAAACCCAGAGAGTTGGTTACGTTT TGCACAGAACCAATTTGATGCAATGTGGTACTCCAGAGGAGCAT ACTCAGAAGTTGGATGTCTGTCACTTGTTGCCAAATGTTGCTAGA TGTGAGAGAACTACCTTGACTTTCTTGCAGAATTTGGAGCACTTG GATGGTATGGTTGCTCCAGAAGTTTGTCCAATGGAAACCGCTGCT TACGTCTCTTCTCACTCTTCTTGA 34 Drosophila RDDPIRPPLKVARSPRPGQCQDVVQDVPNVDVQMLELYDRMSFKDI melanogaster DGGVWKQGWNIKYDPLKYNAHHKLKVFVVPHSHNDPGWIQTFEE ManII YYQHDTKHILSNALRHLHDNPEMKFIWAEISYFARFYHDLGENKKL catalytic QMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLLQLTEGQTWLKQ doman FMNVTPTASWAIDPFGHSPTMPYILQKSGFKNMLIQRTHYSVKKEL (KD) AQQRQLEFLWRQIWDNKGDTALFTHMMPFYSYDIPHTCGPDPKVC CQFDFKRMGSFGLSCPWKVPPRTISDQNVAARSDLLVDQWKKKAE LYRTNVLLIPLGDDFRFKQNTEWDVQRVNYERLFEHINSQAHFNVQ AQFGTLQEYFDAVHQAERAGQAEFPTLSGDFFTYADRSDNYWSGY YTSRPYHKRMDRVLMHYVRAAEMLSAWHSWDGMARIEERLEQAR RELSLFQHHDGITGTAKTHVVVDYEQRMQEALKACQMVMQQSVY RLLTKPSIYSPDFSFSYFTLDDSRWPGSGVEDSRTTIILGEDILPSKHV VMHNTLPHWREQLVDFYVSSPFVSVTDLANNPVEAQVSPVWSWH HDTLTKTIHPQGSTTKYRIIFKARVPPMGLATYVLTISDSKPEHTSYA SNLLLRKNPTSLPLGQYPEDVKFGDPREISLRVGNGPTLAFSEQGLL KSIQLTQDSPHVPVHFKFLKYGVRSHGDRSGAYLFLPNGPASPVELG QPVVLVTKGKLESSVSVGLPSVVHQTIMRGGAPEIRNLVDIGSLDNT EIVMRLETHIDSGDIFYTDLNGLQFIKRRRLDKLPLQANYYPIPSGMF IEDANTRLTLLTGQPLGGSSLASGELEIMQDRRLASDDERGLGQGVL DNKPVLHIYRLVLEKVNNCVRPSKLHPAGYLTSAAHKASQSLLDPL DKFIFAENEWIGAQGQFGGDHPSAREDLDVSVMRRLTKSSAKTQRV GYVLHRTNLMQCGTPEEHTQKLDVCHLLPNVARCERTTLTFLQNLE HLDGMVAPEVCPMETAAYVSSHSS 35 Mouse ATGGCTCCAGCTAGAGAAAACGTTTCCTTGTTCTTCAAGTTGTAC CMP-sialic TGTTTGGCTGTTATGACTTTGGTTGCTGCTGCTTACACTGTTGCTT acid TGAGATACACTAGAACTACTGCTGAGGAGTTGTACTTCTCCACTA transporter CTGCTGTTTGTATCACTGAGGTTATCAAGTTGTTGATCTCCGTTG (MmCST) GTTTGTTGGCTAAGGAGACTGGTTCTTTGGGAAGATTCAAGGCTT Codon CCTTGTCCGAAAACGTTTTGGGTTCCCCAAAGGAGTTGGCTAAGT optimized TGTCTGTTCCATCCTTGGTTTACGCTGTTCAGAACAACATGGCTTT CTTGGCTTTGTCTAACTTGGACGCTGCTGTTTACCAAGTTACTTAC CAGTTGAAGATCCCATGTACTGCTTTGTGTACTGTTTTGATGTTG AACAGAACATTGTCCAAGTTGCAGTGGATCTCCGTTTTCATGTTG TGTGGTGGTGTTACTTTGGTTCAGTGGAAGCCAGCTCAAGCTTCC AAAGTTGTTGTTGCTCAGAACCCATTGTTGGGTTTCGGTGCTATT GCTATCGCTGTTTTGTGTTCCGGTTTCGCTGGTGTTTACTTCGAGA AGGTTTTGAAGTCCTCCGACACTTCTTTGTGGGTTAGAAACATCC AGATGTACTTGTCCGGTATCGTTGTTACTTTGGCTGGTACTTACTT GTCTGACGGTGCTGAGATTCAAGAGAAGGGATTCTTCTACGGTT ACACTTACTATGTTTGGTTCGTTATCTTCTTGGCTTCCGTTGGTGG TTTGTACACTTCCGTTGTTGTTAAGTACACTGACAACATCATGAA GGGATTCTCTGCTGCTGCTGCTATTGTTTTGTCCACTATCGCTTCC GTTTTGTTGTTCGGATTGCAGATCACATTGTCCTTTGCTTTGGGAG CTTTGTTGGTTTGTGTTTCCATCTACTTGTACGGATTGCCAAGACA AGACACTACTTCCATTCAGCAAGAGGCTACTTCCAAGGAGAGAA TCATCGGTGTTTAGTAG 36 Mouse MAPARENVSLFFKLYCLAVMTLVAAAYTVALRYTRTTAEELYFSTT CMP-sialic AVCITEVIKLLISVGLLAKETGSLGRFKASLSENVLGSPKELAKLSVP acid SLVYAVQNNMAFLALSNLDAAVYQVTYQLKIPCTALCTVLMLNRT transporter LSKLQWISVFMLCGGVTLVQWKPAQASKVVVAQNPLLGFGAIAIA (MmCST) VLCSGFAGVYFEKVLKSSDTSLWVRNIQMYLSGIVVTLAGTYLSDG AEIQEKGFFYGYTYYVWFVIFLASVGGLYTSVVVKYTDNIMKGFSA AAAIVLSTIASVLLFGLQITLSFALGALLVCVSIYLYGLPRQDTTSIQQ EATSKERIIGV 37 Human ATGGAAAAGAACGGTAACAACAGAAAGTTGAGAGTTTGTGTTGC UDP- TACTTGTAACAGAGCTGACTACTCCAAGTTGGCTCCAATCATGTT GlcNAc 2- CGGTATCAAGACTGAGCCAGAGTTCTTCGAGTTGGACGTTGTTGT epimerase/ TTTGGGTTCCCACTTGATTGATGACTACGGTAACACTTACAGAAT N- GATCGAGCAGGACGACTTCGACATCAACACTAGATTGCACACTA acetylmannosamine TTGTTAGAGGAGAGGACGAAGCTGCTATGGTTGAATCTGTTGGA kinase TTGGCTTTGGTTAAGTTGCCAGACGTTTTGAACAGATTGAAGCCA (HsGNE) GACATCATGATTGTTCACGGTGACAGATTCGATGCTTTGGCTTTG codon GCTACTTCCGCTGCTTTGATGAACATTAGAATCTTGCACATCGAG opitimized GGTGGTGAAGTTTCTGGTACTATCGACGACTCCATCAGACACGCT ATCACTAAGTTGGCTCACTACCATGTTTGTTGTACTAGATCCGCT GAGCAACACTTGATTTCCATGTGTGAGGACCACGACAGAATTTT GTTGGCTGGTTGTCCATCTTACGACAAGTTGTTGTCCGCTAAGAA CAAGGACTACATGTCCATCATCAGAATGTGGTTGGGTGACGACG TTAAGTCTAAGGACTACATCGTTGCTTTGCAGCACCCAGTTACTA CTGACATCAAGCACTCCATCAAGATGTTCGAGTTGACTTTGGACG CTTTGATCTCCTTCAACAAGAGAACTTTGGTTTTGTTCCCAAACA TTGACGCTGGTTCCAAAGAGATGGTTAGAGTTATGAGAAAGAAG GGTATCGAACACCACCCAAACTTCAGAGCTGTTAAGCACGTTCC ATTCGACCAATTCATCCAGTTGGTTGCTCATGCTGGTTGTATGAT CGGTAACTCCTCCTGTGGTGTTAGAGAAGTTGGTGCTTTCGGTAC TCCAGTTATCAACTTGGGTACTAGACAGATCGGTAGAGAGACTG GAGAAAACGTTTTGCATGTTAGAGATGCTGACACTCAGGACAAG ATTTTGCAGGCTTTGCACTTGCAATTCGGAAAGCAGTACCCATGT TCCAAAATCTACGGTGACGGTAACGCTGTTCCAAGAATCTTGAA GTTTTTGAAGTCCATCGACTTGCAAGAGCCATTGCAGAAGAAGTT CTGTTTCCCACCAGTTAAGGAGAACATCTCCCAGGACATTGACCA CATCTTGGAGACATTGTCCGCTTTGGCTGTTGATTTGGGTGGAAC TAACTTGAGAGTTGCTATCGTTTCCATGAAGGGAGAGATCGTTAA GAAGTACACTCAGTTCAACCCAAAGACTTACGAGGAGAGAATCA ACTTGATCTTGCAGATGTGTGTTGAAGCTGCTGCTGAGGCTGTTA AGTTGAACTGTAGAATCTTGGGTGTTGGTATCTCTACTGGTGGTA GAGTTAATCCAAGAGAGGGTATCGTTTTGCACTCCACTAAGTTGA TTCAGGAGTGGAACTCCGTTGATTTGAGAACTCCATTGTCCGACA CATTGCACTTGCCAGTTTGGGTTGACAACGACGGTAATTGTGCTG CTTTGGCTGAGAGAAAGTTCGGTCAAGGAAAGGGATTGGAGAAC TTCGTTACTTTGATCACTGGTACTGGTATTGGTGGTGGTATCATTC ACCAGCACGAGTTGATTCACGGTTCTTCCTTCTGTGCTGCTGAAT TGGGACACTTGGTTGTTTCTTTGGACGGTCCAGACTGTTCTTGTG GTTCCCACGGTTGTATTGAAGCTTACGCATCAGGAATGGCATTGC AGAGAGAGGCTAAGAAGTTGCACGACGAGGACTTGTTGTTGGTT GAGGGAATGTCTGTTCCAAAGGACGAGGCTGTTGGTGCTTTGCA TTTGATCCAGGCTGCTAAGTTGGGTAATGCTAAGGCTCAGTCCAT CTTGAGAACTGCTGGTACTGCTTTGGGATTGGGTGTTGTTAATAT CTTGCACACTATGAACCCATCCTTGGTTATCTTGTCCGGTGTTTTG GCTTCTCACTACATCCACATCGTTAAGGACGTTATCAGACAGCAA GCTTTGTCCTCCGTTCAAGACGTTGATGTTGTTGTTTCCGACTTGG TTGACCCAGCTTTGTTGGGTGCTGCTTCCATGGTTTTGGACTACA CTACTAGAAGAATCTACTAATAG 38 Human MEKNGNNRKLRVCVATCNRADYSKLAPIMFGIKTEPEFFELDVVVL UDP- GSHLIDDYGNTYRMIEQDDFDINTRLHTIVRGEDEAAMVESVGLAL GlcNAc 2- VKLPDVLNRLKPDIMIVHGDRFDALALATSAALMNIRILHIEGGEVS epimerase/ GTIDDSIRHAITKLAHYHVCCTRSAEQHLISMCEDHDRILLAGCPSY N- DKLLSAKNKDYMSIIRMWLGDDVKSKDYIVALQHPVTTDIKHSIKM acetylmannosamine FELTLDALISFNKRTLVLFPNIDAGSKEMVRVMRKKGIEHHPNFRAV kinase KHVPFDQFIQLVAHAGCMIGNSSCGVREVGAFGTPVINLGTRQIGRE (HsGNE) TGENVLHVRDADTQDKILQALHLQFGKQYPCSKIYGDGNAVPRILK FLKSIDLQEPLQKKFCFPPVKENISQDIDHILETLSALAVDLGGTNLR VAIVSMKGEIVKKYTQFNPKTYEERINLILQMCVEAAAEAVKLNCRI LGVGISTGGRVNPREGIVLHSTKLIQEWNSVDLRTPLSDTLHLPVWV DNDGNCAALAERKFGQGKGLENFVTLITGTGIGGGIIHQHELIHGSS FCAAELGHLVVSLDGPDCSCGSHGCIEAYASGMALQREAKKLHDE DLLLVEGMSVPKDEAVGALHLIQAAKLGNAKAQSILRTAGTALGLG VVNILHTMNPSLVILSGVLASHYIHIVKDVIRQQALSSVQDVDVVVS DLVDPALLGAASMVLDYTTRRIY 39 Human ATGGACTCTGTTGAAAAGGGTGCTGCTACTTCTGTTTCCAACCCA CMP-sialic AGAGGTAGACCATCCAGAGGTAGACCTCCTAAGTTGCAGAGAAA acid CTCCAGAGGTGGTCAAGGTAGAGGTGTTGAAAAGCCACCACACT synthase TGGCTGCTTTGATCTTGGCTAGAGGAGGTTCTAAGGGTATCCCAT (HsCSS) TGAAGAACATCAAGCACTTGGCTGGTGTTCCATTGATTGGATGG codon GTTTTGAGAGCTGCTTTGGACTCTGGTGCTTTCCAATCTGTTTGG optimized GTTTCCACTGACCACGACGAGATTGAGAACGTTGCTAAGCAATT CGGTGCTCAGGTTCACAGAAGATCCTCTGAGGTTTCCAAGGACTC TTCTACTTCCTTGGACGCTATCATCGAGTTCTTGAACTACCACAA CGAGGTTGACATCGTTGGTAACATCCAAGCTACTTCCCCATGTTT GCACCCAACTGACTTGCAAAAAGTTGCTGAGATGATCAGAGAAG AGGGTTACGACTCCGTTTTCTCCGTTGTTAGAAGGCACCAGTTCA GATGGTCCGAGATTCAGAAGGGTGTTAGAGAGGTTACAGAGCCA TTGAACTTGAACCCAGCTAAAAGACCAAGAAGGCAGGATTGGGA CGGTGAATTGTACGAAAACGGTTCCTTCTACTTCGCTAAGAGACA CTTGATCGAGATGGGATACTTGCAAGGTGGAAAGATGGCTTACT ACGAGATGAGAGCTGAACACTCCGTTGACATCGACGTTGATATC GACTGGCCAATTGCTGAGCAGAGAGTTTTGAGATACGGTTACTTC GGAAAGGAGAAGTTGAAGGAGATCAAGTTGTTGGTTTGTAACAT CGACGGTTGTTTGACTAACGGTCACATCTACGTTTCTGGTGACCA GAAGGAGATTATCTCCTACGACGTTAAGGACGCTATTGGTATCTC CTTGTTGAAGAAGTCCGGTATCGAAGTTAGATTGATCTCCGAGA GAGCTTGTTCCAAGCAAACATTGTCCTCTTTGAAGTTGGACTGTA AGATGGAGGTTTCCGTTTCTGACAAGTTGGCTGTTGTTGACGAAT GGAGAAAGGAGATGGGTTTGTGTTGGAAGGAAGTTGCTTACTTG GGTAACGAAGTTTCTGACGAGGAGTGTTTGAAGAGAGTTGGTTT GTCTGGTGCTCCAGCTGATGCTTGTTCCACTGCTCAAAAGGCTGT TGGTTACATCTGTAAGTGTAACGGTGGTAGAGGTGCTATTAGAG AGTTCGCTGAGCACATCTGTTTGTTGATGGAGAAAGTTAATAACT CCTGTCAGAAGTAGTAG 40 Human MDSVEKGAATSVSNPRGRPSRGRPPKLQRNSRGGQGRGVEKPPHLA CMP-sialic ALILARGGSKGIPLKNIKHLAGVPLIGWVLRAALDSGAFQSVWVST acid DHDEIENVAKQFGAQVHRRSSEVSKDSSTSLDAIIEFLNYHNEVDIV synthase GNIQATSPCLHPTDLQKVAEMIREEGYDSVFSVVRRHQFRWSEIQK (HsCSS) GVREVTEPLNLNPAKRPRRQDWDGELYENGSFYFAKRHLIEMGYL QGGKMAYYEMRAEHSVDIDVDIDWPIAEQRVLRYGYFGKEKLKEI KLLVCNIDGCLTNGHIYVSGDQKEIISYDVKDAIGISLLKKSGIEVRLI SERACSKQTLSSLKLDCKMEVSVSDKLAVVDEWRKEMGLCWKEV AYLGNEVSDEECLKRVGLSGAPADACSTAQKAVGYICKCNGGRGA IREFAEHICLLMEKVNNSCQK 41 Human N- ATGCCATTGGAATTGGAGTTGTGTCCTGGTAGATGGGTTGGTGGT acetylneuraminate- CAACACCCATGTTTCATCATCGCTGAGATCGGTCAAAACCACCA 9- AGGAGACTTGGACGTTGCTAAGAGAATGATCAGAATGGCTAAGG phosphate AATGTGGTGCTGACTGTGCTAAGTTCCAGAAGTCCGAGTTGGAG synthase TTCAAGTTCAACAGAAAGGCTTTGGAAAGACCATACACTTCCAA (HsSPS) GCACTCTTGGGGAAAGACTTACGGAGAACACAAGAGACACTTGG codon AGTTCTCTCACGACCAATACAGAGAGTTGCAGAGATACGCTGAG optimized GAAGTTGGTATCTTCTTCACTGCTTCTGGAATGGACGAAATGGCT GTTGAGTTCTTGCACGAGTTGAACGTTCCATTCTTCAAAGTTGGT TCCGGTGACACTAACAACTTCCCATACTTGGAAAAGACTGCTAA GAAAGGTAGACCAATGGTTATCTCCTCTGGAATGCAGTCTATGG ACACTATGAAGCAGGTTTACCAGATCGTTAAGCCATTGAACCCA AACTTTTGTTTCTTGCAGTGTACTTCCGCTTACCCATTGCAACCAG AGGACGTTAATTTGAGAGTTATCTCCGAGTACCAGAAGTTGTTCC CAGACATCCCAATTGGTTACTCTGGTCACGAGACTGGTATTGCTA TTTCCGTTGCTGCTGTTGCTTTGGGTGCTAAGGTTTTGGAGAGAC ACATCACTTTGGACAAGACTTGGAAGGGTTCTGATCACTCTGCTT CTTTGGAACCTGGTGAGTTGGCTGAACTTGTTAGATCAGTTAGAT TGGTTGAGAGAGCTTTGGGTTCCCCAACTAAGCAATTGTTGCCAT GTGAGATGGCTTGTAACGAGAAGTTGGGAAAGTCCGTTGTTGCT AAGGTTAAGATCCCAGAGGGTACTATCTTGACTATGGACATGTT GACTGTTAAAGTTGGAGAGCCAAAGGGTTACCCACCAGAGGACA TCTTTAACTTGGTTGGTAAAAAGGTTTTGGTTACTGTTGAGGAGG ACGACACTATTATGGAGGAGTTGGTTGACAACCACGGAAAGAAG ATCAAGTCCTAG 42 Human N- MPLELELCPGRWVGGQHPCFIIAEIGQNHQGDLDVAKRMIRMAKEC acetylneuraminate- GADCAKFQKSELEFKFNRKALERPYTSKHSWGKTYGEHKRHLEFSH 9- DQYRELQRYAEEVGIFFTASGMDEMAVEFLHELNVPFFKVGSGDTN phosphate NFPYLEKTAKKGRPMVISSGMQSMDTMKQVYQIVKPLNPNFCFLQC synthase TSAYPLQPEDVNLRVISEYQKLFPDIPIGYSGHETGIAISVAAVALGA (HsSPS) KVLERHITLDKTWKGSDHSASLEPGELAELVRSVRLVERALGSPTK QLLPCEMACNEKLGKSVVAKVKIPEGTILTMDMLTVKVGEPKGYPP EDIFNLVGKKVLVTVEEDDTIMEELVDNHGKKIKS 43 Mouse GTTTTTCAAATGCCAAAGTCCCAGGAGAAAGTTGCTGTTGGTCCA alpha-2,6- GCTCCACAAGCTGTTTTCTCCAACTCCAAGCAAGATCCAAAGGA sialyl GGGTGTTCAAATCTTGTCCTACCCAAGAGTTACTGCTAAGGTTAA transferase GCCACAACCATCCTTGCAAGTTTGGGACAAGGACTCCACTTACTC catalytic CAAGTTGAACCCAAGATTGTTGAAGATTTGGAGAAACTACTTGA domain ACATGAACAAGTACAAGGTTTCCTACAAGGGTCCAGGTCCAGGT (MmmST6) GTTAAGTTCTCCGTTGAGGCTTTGAGATGTCACTTGAGAGACCAC codon GTTAACGTTTCCATGATCGAGGCTACTGACTTCCCATTCAACACT optimized ACTGAATGGGAGGGATACTTGCCAAAGGAGAACTTCAGAACTAA GGCTGGTCCATGGCATAAGTGTGCTGTTGTTTCTTCTGCTGGTTC CTTGAAGAACTCCCAGTTGGGTAGAGAAATTGACAACCACGACG CTGTTTTGAGATTCAACGGTGCTCCAACTGACAACTTCCAGCAGG ATGTTGGTACTAAGACTACTATCAGATTGGTTAACTCCCAATTGG TTACTACTGAGAAGAGATTCTTGAAGGACTCCTTGTACACTGAGG GAATCTTGATTTTGTGGGACCCATCTGTTTACCACGCTGACATTC CACAATGGTATCAGAAGCCAGACTACAACTTCTTCGAGACTTAC AAGTCCTACAGAAGATTGCACCCATCCCAGCCATTCTACATCTTG AAGCCACAAATGCCATGGGAATTGTGGGACATCATCCAGGAAAT TTCCCCAGACTTGATCCAACCAAACCCACCATCTTCTGGAATGTT GGGTATCATCATCATGATGACTTTGTGTGACCAGGTTGACATCTA CGAGTTCTTGCCATCCAAGAGAAAGACTGATGTTTGTTACTACCA CCAGAAGTTCTTCGACTCCGCTTGTACTATGGGAGCTTACCACCC ATTGTTGTTCGAGAAGAACATGGTTAAGCACTTGAACGAAGGTA CTGACGAGGACATCTACTTGTTCGGAAAGGCTACTTTGTCCGGTT TCAGAAACAACAGATGTTAG 44 Mouse VFQMPKSQEKVAVGPAPQAVFSNSKQDPKEGVQILSYPRVTAKVKP alpha-2,6- QPSLQVWDKDSTYSKLNPRLLKIWRNYLNMNKYKVSYKGPGPGVK sialyl FSVEALRCHLRDHVNVSMIEATDFPFNTTEWEGYLPKENFRTKAGP transferase WHKCAVVSSAGSLKNSQLGREIDNHDAVLRFNGAPTDNFQQDVGT catalytic KTTIRLVNSQLVTTEKRFLKDSLYTEGILILWDPSVYHADIPQWYQK domain PDYNFFETYKS (MmmST6) YRRLHPSQPFYILKPQMPWELWDIIQEISPDLIQPNPPSSGMLGIIIMM TLCDQVDIYEFLPSKRKTDVCYYHQKFFDSACTMGAYHPLLFEKNM VKHLNEGTDEDIYLFGKATLSGFRNNRC 45 Sequence AAATGCGTACCTCTTCTACGAGATTCAAGCGAATGAGAATAATG of the TAATATGCAAGATCAGAAAGAATGAAAGGAGTTGAAAAAAAAA PpPMA1 ACCGTTGCGTTTTGACCTTGAATGGGGTGGAGGTTTCCATTCAAA promoter: GTAAAGCCTGTGTCTTGGTATTTTCGGCGGCACAAGAAATCGTAA TTTTCATCTTCTAAACGATGAAGATCGCAGCCCAACCTGTATGTA GTTAACCGGTCGGAATTATAAGAAAGATTTTCGATCAACAAACC CTAGCAAATAGAAAGCAGGGTTACAACTTTAAACCGAAGTCACA AACGATAAACCACTCAGCTCCCACCCAAATTCATTCCCACTAGCA GAAAGGAATTATTTAATCCCTCAGGAAACCTCGATGATTCTCCCG TTCTTCCATGGGCGGGTATCGCAAAATGAGGAATTTTTCAAATTT CTCTATTGTCAAGACTGTTTATTATCTAAGAAATAGCCCAATCCG AAGCTCAGTTTTGAAAAAATCACTTCCGCGTTTCTTTTTTACAGC CCGATGAATATCCAAATTTGGAATATGGATTACTCTATCGGGACT GCAGATAATATGACAACAACGCAGATTACATTTTAGGTAAGGCA TAAACACCAGCCAGAAATGAAACGCCCACTAGCCATGGTCGAAT AGTCCAATGAATTCAGATAGCTATGGTCTAAAAGCTGATGTTTTT TATTGGGTAATGGCGAAGAGTCCAGTACGACTTCCAGCAGAGCT GAGATGGCCATTTTTGGGGGTATTAGTAACTTTTTGAGCTCTTTT CACTTCGATGAAGTGTCCCATTCGGGATATAATCGGATCGCGTCG TTTTCTCGAAAATACAGCTTAGCGTCGTCCGCTTGTTGTAAAAGC AGCACCACATTCCTAATCTCTTATATAAACAAAACAACCCAAATT ATCAGTGCTGTTTTCCCACCAGATATAAGTTTCTTTTCTCTTCCGC TTTTTGATTTTTTATCTCTTTCCTTTAAAAACTTCTTTACCTTAAAG GGCGGCC 46 Sequence TAAGCTTCACGATTTGTGTTCCAGTTTATCCCCCCTTTATATACCG of the TTAACCCTTTCCCTGTTGAGCTGACTGTTGTTGTATTACCGCAATT PpPMA1 TTTCCAAGTTTGCCATGCTTTTCGTGTTATTTGACCGATGTCTTTT terminator: TTCCCAAATCAAACTATATTTGTTACCATTTAAACCAAGTTATCT TTTGTATTAAGAGTCTAAGTTTGTTCCCAGGCTTCATGTGAGAGT GATAACCATCCAGACTATGATTCTTGTTTTTTATTGGGTTTGTTTG TGTGATACATCTGAGTTGTGATTCGTAAAGTATGTCAGTCTATCT AGATTTTTAATAGTTAATTGGTAATCAATGACTTGTTTGTTTTAAC TTTTAAATTGTGGGTCGTATCCACGCGTTTAGTATAGCTGTTCAT GGCTGTTAGAGGAGGGCGATGTTTATATACAGAGGACAAGAATG AGGAGGCGGCGTGTATTTTTAAAATGGAGACGCGACTCCTGTAC ACCTTATCGGTTGG 47 Sequence TGGACACAGGAGACTCAGAAACAGACACAGAGCGTTCTGAGTCC of the TGGTGCTCCTGACGTAGGCCTAGAACAGGAATTATTGGCTTTATT PpOCH1 TGTTTGTCCATTTCATAGGCTTGGGGTAATAGATAGATGACAGAG promoter: AAATAGAGAAGACCTAATATTTTTTGTTCATGGCAAATCGCGGGT TCGCGGTCGGGTCACACACGGAGAAGTAATGAGAAGAGCTGGTA ATCTGGGGTAAAAGGGTTCAAAAGAAGGTCGCCTGGTAGGGATG CAATACAAGGTTGTCTTGGAGTTTACATTGACCAGATGATTTGGC TTTTTCTCTGTTCAATTCACATTTTTCAGCGAGAATCGGATTGACG GAGAAATGGCGGGGTGTGGGGTGGATAGATGGCAGAAATGCTC GCAATCACCGCGAAAGAAAGACTTTATGGAATAGAACTACTGGG TGGTGTAAGGATTACATAGCTAGTCCAATGGAGTCCGTTGGAAA GGTAAGAAGAAGCTAAAACCGGCTAAGTAACTAGGGAAGAATG ATCAGACTTTGATTTGATGAGGTCTGAAAATACTCTGCTGCTTTT TCAGTTGCTTTTTCCCTGCAACCTATCATTTTCCTTTTCATAAGCC TGCCTTTTCTGTTTTCACTTATATGAGTTCCGCCGAGACTTCCCCA AATTCTCTCCTGGAACATTCTCTATCGCTCTCCTTCCAAGTTGCGC CCCCTGGCACTGCCTAGTAATATTACCACGCGACTTATATTCAGT TCCACAATTTCCAGTGTTCGTAGCAAATATCATCAGCC 48 Sequence AATATATACCTCATTTGTTCAATTTGGTGTAAAGAGTGTGGCGGA of the TAGACTTCTTGTAAATCAGGAAAGCTACAATTCCAATTGCTGCAA PpALG12 AAAATACCAATGCCCATAAACCAGTATGAGCGGTGCCTTCGACG terminator: GATTGCTTACTTTCCGACCCTTTGTCGTTTGATTCTTCTGCCTTTG GTGAGTCAGTTTGTTTCGACTTTATATCTGACTCATCAACTTCCTT TACGGTTGCGTTTTTAATCATAATTTTAGCCGTTGGCTTATTATCC CTTGAGTTGGTAGGAGTTTTGATGATGCTG 49 Sequence GAAGTAAAGTTGGCGAAACTTTGGGAACCTTTGGTTAAAACTTT of the GTAATTTTTGTCGCTACCCATTAGGCAGAATCTGCATCTTGGGAG PpSEC4 GGGGATGTGGTGGCGTTCTGAGATGTACGCGAAGAATGAAGAGC promoter: CAGTGGTAACAACAGGCCTAGAGAGATACGGGCATAATGGGTAT AACCTACAAGTTAAGAATGTAGCAGCCCTGGAAACCAGATTGAA ACGAAAAACGAAATCATTTAAACTGTAGGATGTTTTGGCTCATTG TCTGGAAGGCTGGCTGTTTATTGCCCTGTTCTTTGCATGGGAATA AGCTATTATATCCCTCACATAATCCCAGAAAATAGATTGAAGCA ACGCGAAATCCTTACGTATCGAAGTAGCCTTCTTACACATTCACG TTGTACGGATAAGAAAACTACTCAAACGAACAATC 50 Sequence AATAGATATAGCGAGATTAGAGAATGAATACCTTCTTCTAAGCG of the ATCGTCCGTCATCATAGAATATCATGGACTGTATAGTTTTTTTTTT PpOCH1 GTACATATAATGATTAAACGGTCATCCAACATCTCGTTGACAGAT terminator: CTCTCAGTACGCGAAATCCCTGACTATCAAAGCAAGAACCGATG AAGAAAAAAACAACAGTAACCCAAACACCACAACAAACACTTT ATCTTCTCCCCCCCAACACCAATCATCAAAGAGATGTCGGAACA CAAACACCAAGAAGCAAAAACTAACCCCATATAAAAACATCCTG GTAGATAATGCTGGTAACCCGCTCTCCTTCCATATTCTGGGCTAC TTCACGAAGTCTGACCGGTCTCAGTTGATCAACATGATCCTCGAA ATGG 51 Sequence TTAAGGTTTGGAACAACACTAAACTACCTTGCGGTACTACCATTG of the ACACTACACATCCTTAATTCCAATCCTGTCTGGCCTCCTTCACCTT PpTEF1 TTAACCATCTTGCCCATTCCAACTCGTGTCAGATTGCGTATCAAG promoter TGAAAAAAAAAAAATTTTAAATCTTTAACCCAATCAGGTAATAA CTGTCGCCTCTTTTATCTGCCGCACTGCATGAGGTGTCCCCTTAGT GGGAAAGAGTACTGAGCCAACCCTGGAGGACAGCAAGGGAAAA ATACCTACAACTTGCTTCATAATGGTCGTAAAAACAATCCTTGTC GGATATAAGTGTTGTAGACTGTCCCTTATCCTCTGCGATGTTCTT CCTCTCAAAGTTTGCGATTTCTCTCTATCAGAATTGCCATCAAGA GACTCAGGACTAATTTCGCAGTCCCACACGCACTCGTACATGATT GGCTGAAATTTCCCTAAAGAATTTCTTTTTCACGAAAATTTTTTTT TTACACAAGATTTTCAGCAGATATAAAATGGAGAGCAGGACCTC CGCTGTGACTCTTCTTTTTTTTCTTTTATTCTCACTACATACATTTT AGTTATTCGCCAAC 52 Sequence ATTGCTTGAAGCTTTAATTTATTTTATTAACATAATAATAATACA of the AGCATGATATATTTGTATTTTGTTCGTTAACATTGATGTTTTCTTC PpTEF1 ATTTACTGTTATTGTTTGTAACTTTGATCGATTTATCTTTTCTACTT terminator: TACTGTAATATGGCTGGCGGGTGAGCCTTGAACTCCCTGTATTAC TTTACCTTGCTATTACTTAATCTATTGACTAGCAGCGACCTCTTCA ACCGAAGGGCAAGTACACAGCAAGTTCATGTCTCCGTAAGTGTC ATCAACCCTGGAAACAGTGGGCCATGTC 53 Sequence TTTTTGTAGAAATGTCTTGGTGTCCTCGTCCAATCAGGTAGCCAT of the CTCTGAAATATCTGGCTCCGTTGCAACTCCGAACGACCTGCTGGC PpGAPDH AACGTAAAATTCTCCGGGGTAAAACTTAAATGTGGAGTAATGGA promoter: ACCAGAAACGTCTCTTCCCTTCTCTCTCCTTCCACCGCCCGTTACC GTCCCTAGGAAATTTTACTCTGCTGGAGAGCTTCTTCTACGGCCC CCTTGCAGCAATGCTCTTCCCAGCATTACGTTGCGGGTAAAACGG AGGTCGTGTACCCGACCTAGCAGCCCAGGGATGGAAAAGTCCCG GCCGTCGCTGGCAATAATAGCGGGCGGACGCATGTCATGAGATT ATTGGAAACCACCAGAATCGAATATAAAAGGCGAACACCTTTCC CAATTTTGGTTTCTCCTGACCCAAAGACTTTAAATTTAATTTATTT GTCCCTATTTCAATCAATTGAACAACTATCAAAACACA 54 Sequence ATTTACAATTAGTAATATTAAGGTGGTAAAAACATTCGTAGAATT of the GAAATGAATTAATATAGTATGACAATGGTTCATGTCTATAAATCT PpALG3 CCGGCTTCGGTACCTTCTCCCCAATTGAATACATTGTCAAAATGA terminator: ATGGTTGAACTATTAGGTTCGCCAGTTTCGTTATTAAGAAAACTG TTAAAATCAAATTCCATATCATCGGTTCCAGTGGGAGGACCAGTT CCATCGCCAAAATCCTGTAAGAATCCATTGTCAGAACCTGTAAA GTCAGTTTGAGATGAAATTTTTCCGGTCTTTGTTGACTTGGAAGC TTCGTTAAGGTTAGGTGAAACAGTTTGATCAACCAGCGGCTCCCG TTTTCGTCGCTTAGTAG 55 Sequence AACATCCAAAGACGAAAGGTTGAATGAAACCTTTTTGCCATCCG of the ACATCCACAGGTCCATTCTCACACATAAGTGCCAAACGCAACAG PpAOX1 GAGGGGATACACTAGCAGCAGACCGTTGCAAACGCAGGACCTCC promoter ACTCCTCTTCTCCTCAACACCCACTTTTGCCATCGAAAAACCAGC and CCAGTTATTGGGCTTGATTGGAGCTCGCTCATTCCAATTCCTTCT integration ATTAGGCTACTAACACCATGACTTTATTAGCCTGTCTATCCTGGC locus: CCCCCTGGCGAGGTTCATGTTTGTTTATTTCCGAATGCAACAAGC TCCGCATTACACCCGAACATCACTCCAGATGAGGGCTTTCTGAGT GTGGGGTCAAATAGTTTCATGTTCCCCAAATGGCCCAAAACTGA CAGTTTAAACGCTGTCTTGGAACCTAATATGACAAAAGCGTGAT CTCATCCAAGATGAACTAAGTTTGGTTCGTTGAAATGCTAACGGC CAGTTGGTCAAAAAGAAACTTCCAAAAGTCGGCATACCGTTTGT CTTGTTTGGTATTGATTGACGAATGCTCAAAAATAATCTCATTAA TGCTTAGCGCAGTCTCTCTATCGCTTCTGAACCCCGGTGCACCTG TGCCGAAACGCAAATGGGGAAACACCCGCTTTTTGGATGATTAT GCATTGTCTCCACATTGTATGCTTCCAAGATTCTGGTGGGAATAC TGCTGATAGCCTAACGTTCATGATCAAAATTTAACTGTTCTAACC CCTACTTGACAGCAATATATAAACAGAAGGAAGCTGCCCTGTCT TAAACCTTTTTTTTTATCATCATTATTAGCTTACTTTCATAATTGC GACTGGTTCCAATTGACAAGCTTTTGATTTTAACGACTTTTAACG ACAACTTGAGAAGATCAAAAAACAACTAATTATTCGAAACG 56 Sequence ACAGGCCCCTTTTCCTTTGTCGATATCATGTAATTAGTTATGTCAC of the GCTTACATTCACGCCCTCCTCCCACATCCGCTCTAACCGAAAAGG ScCYC1 AAGGAGTTAGACAACCTGAAGTCTAGGTCCCTATTTATTTTTTTT terminator: AATAGTTATGTTAGTATTAAGAACGTTATTTATATTTCAAATTTTT CTTTTTTTTCTGTACAAACGCGTGTACGCATGTAACATTATACTG AAAACCTTGCTTGAGAAGGTTTTGGGACGCTCGAAGGCTTTAATT TGCAAGCTGCCGGCTCTTAAG 57 Sequence GATCCCCCACACACCATAGCTTCAAAATGTTTCTACTCCTTTTTTA of the CTCTTCCAGATTTTCTCGGACTCCGCGCATCGCCGTACCACTTCA ScTEF1 AAACACCCAAGCACAGCATACTAAATTTCCCCTCTTTCTTCCTCT promoter: AGGGTGTCGTTAATTACCCGTACTAAAGGTTTGGAAAAGAAAAA AGAGACCGCCTCGTTTCTTTTTCTTCGTCGAAAAAGGCAATAAAA ATTTTTATCACGTTTCTTTTTCTTGAAAATTTTTTTTTTTGATTTTT TTCTCTTTCGATGACCTCCCATTGATATTTAAGTTAATAAACGGT CTTCAATTTCTCAAGTTTCAGTTTCATTTTTCTTGTTCTATTACAA CTTTTTTTACTTCTTGCTCATTAGAAAGAAAGCATAGCAATCTAA TCTAAGTTTTAATTACAAA 58 Sequence ATGGCCAAGTTGACCAGTGCCGTTCCGGTGCTCACCGCGCGCGA of the Shble CGTCGCCGGAGCGGTCGAGTTCTGGACCGACCGGCTCGGGTTCT ORF CCCGGGACTTCGTGGAGGACGACTTCGCCGGTGTGGTCCGGGAC (Zeocin GACGTGACCCTGTTCATCAGCGCGGTCCAGGACCAGGTGGTGCC resistance GGACAACACCCTGGCCTGGGTGTGGGTGCGCGGCCTGGACGAGC marker): TGTACGCCGAGTGGTCGGAGGTCGTGTCCACGAACTTCCGGGAC GCCTCCGGGCCGGCCATGACCGAGATCGGCGAGCAGCCGTGGGG GCGGGAGTTCGCCCTGCGCGACCCGGCCGGCAACTGCGTGCACT TCGTGGCCGAGGAGCAGGACTGA 59 Sequence ATCGGCCTTTGTTGATGCAAGTTTTACGTGGATCATGGACTAAGG of the 5′- AGTTTTATTTGGACCAAGTTCATCGTCCTAGACATTACGGAAAGG Region GTTCTGCTCCTCTTTTTGGAAACTTTTTGGAACCTCTGAGTATGAC used for AGCTTGGTGGATTGTACCCATGGTATGGCTTCCTGTGAATTTCTA knock out TTTTTTCTACATTGGATTCACCAATCAAAACAAATTAGTCGCCAT of GGCTTTTTGGCTTTTGGGTCTATTTGTTTGGACCTTCTTGGAATAT PpURA5: GCTTTGCATAGATTTTTGTTCCACTTGGACTACTATCTTCCAGAG AATCAAATTGCATTTACCATTCATTTCTTATTGCATGGGATACAC CACTATTTACCAATGGATAAATACAGATTGGTGATGCCACCTACA CTTTTCATTGTACTTTGCTACCCAATCAAGACGCTCGTCTTTTCTG TTCTACCATATTACATGGCTTGTTCTGGATTTGCAGGTGGATTCCT GGGCTATATCATGTATGATGTCACTCATTACGTTCTGCATCACTC CAAGCTGCCTCGTTATTTCCAAGAGTTGAAGAAATATCATTTGGA ACATCACTACAAGAATTACGAGTTAGGCTTTGGTGTCACTTCCAA ATTCTGGGACAAAGTCTTTGGGACTTATCTGGGTCCAGACGATGT GTATCAAAAGACAAATTAGAGTATTTATAAAGTTATGTAAGCAA ATAGGGGCTAATAGGGAAAGAAAAATTTTGGTTCTTTATCAGAG CTGGCTCGCGCGCAGTGTTTTTCGTGCTCCTTTGTAATAGTCATTT TTGACTACTGTTCAGATTGAAATCACATTGAAGATGTCACTCGAG GGGTACCAAAAAAGGTTTTTGGATGCTGCAGTGGCTTCGC 60 Sequence GGTCTTTTCAACAAAGCTCCATTAGTGAGTCAGCTGGCTGAATCT of the 3′- TATGCACAGGCCATCATTAACAGCAACCTGGAGATAGACGTTGT Region ATTTGGACCAGCTTATAAAGGTATTCCTTTGGCTGCTATTACCGT used for GTTGAAGTTGTACGAGCTCGGCGGCAAAAAATACGAAAATGTCG knock out GATATGCGTTCAATAGAAAAGAAAAGAAAGACCACGGAGAAGG of TGGAAGCATCGTTGGAGAAAGTCTAAAGAATAAAAGAGTACTGA PpURA5: TTATCGATGATGTGATGACTGCAGGTACTGCTATCAACGAAGCAT TTGCTATAATTGGAGCTGAAGGTGGGAGAGTTGAAGGTAGTATT ATTGCCCTAGATAGAATGGAGACTACAGGAGATGACTCAAATAC CAGTGCTACCCAGGCTGTTAGTCAGAGATATGGTACCCCTGTCTT GAGTATAGTGACATTGGACCATATTGTGGCCCATTTGGGCGAAA CTTTCACAGCAGACGAGAAATCTCAAATGGAAACGTATAGAAAA AAGTATTTGCCCAAATAAGTATGAATCTGCTTCGAATGAATGAAT TAATCCAATTATCTTCTCACCATTATTTTCTTCTGTTTCGGAGCTT TGGGCACGGCGGCGGGTGGTGCGGGCTCAGGTTCCCTTTCATAA ACAGATTTAGTACTTGGATGCTTAATAGTGAATGGCGAATGCAA AGGAACAATTTCGTTCATCTTTAACCCTTTCACTCGGGGTACACG TTCTGGAATGTACCCGCCCTGTTGCAACTCAGGTGGACCGGGCA ATTCTTGAACTTTCTGTAACGTTGTTGGATGTTCAACCAGAAATT GTCCTACCAACTGTATTAGTTTCCTTTTGGTCTTATATTGTTCATC GAGATACTTCCCACTCTCCTTGATAGCCACTCTCACTCTTCCTGG ATTACCAAAATCTTGAGGATGAGTCTTTTCAGGCTCCAGGATGCA AGGTATATCCAAGTACCTGCAAGCATCTAATATTGTCTTTGCCAG GGGGTTCTCCACACCATACTCCTTTTGGCGCATGC 61 Sequence TCTAGAGGGACTTATCTGGGTCCAGACGATGTGTATCAAAAGAC of the AAATTAGAGTATTTATAAAGTTATGTAAGCAAATAGGGGCTAAT PpURA5 AGGGAAAGAAAAATTTTGGTTCTTTATCAGAGCTGGCTCGCGCG auxotrophic CAGTGTTTTTCGTGCTCCTTTGTAATAGTCATTTTTGACTACTGTT marker: CAGATTGAAATCACATTGAAGATGTCACTGGAGGGGTACCAAAA AAGGTTTTTGGATGCTGCAGTGGCTTCGCAGGCCTTGAAGTTTGG AACTTTCACCTTGAAAAGTGGAAGACAGTCTCCATACTTCTTTAA CATGGGTCTTTTCAACAAAGCTCCATTAGTGAGTCAGCTGGCTGA ATCTTATGCTCAGGCCATCATTAACAGCAACCTGGAGATAGACG TTGTATTTGGACCAGCTTATAAAGGTATTCCTTTGGCTGCTATTA CCGTGTTGAAGTTGTACGAGCTGGGCGGCAAAAAATACGAAAAT GTCGGATATGCGTTCAATAGAAAAGAAAAGAAAGACCACGGAG AAGGTGGAAGCATCGTTGGAGAAAGTCTAAAGAATAAAAGAGT ACTGATTATCGATGATGTGATGACTGCAGGTACTGCTATCAACGA AGCATTTGCTATAATTGGAGCTGAAGGTGGGAGAGTTGAAGGTT GTATTATTGCCCTAGATAGAATGGAGACTACAGGAGATGACTCA AATACCAGTGCTACCCAGGCTGTTAGTCAGAGATATGGTACCCCT GTCTTGAGTATAGTGACATTGGACCATATTGTGGCCCATTTGGGC GAAACTTTCACAGCAGACGAGAAATCTCAAATGGAAACGTATAG AAAAAAGTATTTGCCCAAATAAGTATGAATCTGCTTCGAATGAA TGAATTAATCCAATTATCTTCTCACCATTATTTTCTTCTGTTTCGG AGCTTTGGGCACGGCGGCGGATCC 62 Sequence CCTGCACTGGATGGTGGCGCTGGATGGTAAGCCGCTGGCAAGCG of the part GTGAAGTGCCTCTGGATGTCGCTCCACAAGGTAAACAGTTGATT of the Ec GAACTGCCTGAACTACCGCAGCCGGAGAGCGCCGGGCAACTCTG lacZ gene GCTCACAGTACGCGTAGTGCAACCGAACGCGACCGCATGGTCAG that was AAGCCGGGCACATCAGCGCCTGGCAGCAGTGGCGTCTGGCGGAA used to AACCTCAGTGTGACGCTCCCCGCCGCGTCCCACGCCATCCCGCAT construct CTGACCACCAGCGAAATGGATTTTTGCATCGAGCTGGGTAATAA the GCGTTGGCAATTTAACCGCCAGTCAGGCTTTCTTTCACAGATGTG PpURA5 GATTGGCGATAAAAAACAACTGCTGACGCCGCTGCGCGATCAGT blaster TCACCCGTGCACCGCTGGATAACGACATTGGCGTAAGTGAAGCG (recyelable ACCCGCATTGACCCTAACGCCTGGGTCGAACGCTGGAAGGCGGC auxotrophic GGGCCATTACCAGGCCGAAGCAGCGTTGTTGCAGTGCACGGCAG marker) ATACACTTGCTGATGCGGTGCTGATTACGACCGCTCACGCGTGGC AGCATCAGGGGAAAACCTTATTTATCAGCCGGAAAACCTACCGG ATTGATGGTAGTGGTCAAATGGCGATTACCGTTGATGTTGAAGTG GCGAGCGATACACCGCATCCGGCGCGGATTGGCCTGAACTGCCAG 63 PpURA5 MSLEGYQKRFLDAAVASQALKFGTFTLKSGRQSPYFFNMGLFNKAP amino acid LVSQLAESYAQAIINSNLEIDVVFGPAYKGIPLAAITVLKLYELGGKK sequence YENVGYAFNRKEKKDHGEGGSIVGESLKNKRVLIIDDVMTAGTAIN EAFAIIGAEGGRVEGCIIALDRMETTGDDSNTSATQAVSQRYGTPVL SIVTLDHIVAHLGETFTADEKSQMETYRKKYLPKZ 64 Sequence AAAACCTTTTTTCCTATTCAAACACAAGGCATTGCTTCAACACGT of the 5′- GTGCGTATCCTTAACACAGATACTCCATACTTCTAATAATGTGAT Region AGACGAATACAAAGATGTTCACTCTGTGTTGTGTCTACAAGCATT used for TCTTATTCTGATTGGGGATATTCTAGTTACAGCACTAAACAACTG knock out GCGATACAAACTTAAATTAAATAATCCGAATCTAGAAAATGAAC of TTTTGGATGGTCCGCCTGTTGGTTGGATAAATCAATACCGATTAA PpOCH1: ATGGATTCTATTCCAATGAGAGAGTAATCCAAGACACTCTGATGT CAATAATCATTTGCTTGCAACAACAAACCCGTCATCTAATCAAAG GGTTTGATGAGGCTTACCTTCAATTGCAGATAAACTCATTGCTGT CCACTGCTGTATTATGTGAGAATATGGGTGATGAATCTGGTCTTC TCCACTCAGCTAACATGGCTGTTTGGGCAAAGGTGGTACAATTAT ACGGAGATCAGGCAATAGTGAAATTGTTGAATATGGCTACTGGA CGATGCTTCAAGGATGTACGTCTAGTAGGAGCCGTGGGAAGATT GCTGGCAGAACCAGTTGGCACGTCGCAACAATCCCCAAGAAATG AAATAAGTGAAAACGTAACGTCAAAGACAGCAATGGAGTCAAT ATTGATAACACCACTGGCAGAGCGGTTCGTACGTCGTTTTGGAGC CGATATGAGGCTCAGCGTGCTAACAGCACGATTGACAAGAAGAC TCTCGAGTGACAGTAGGTTGAGTAAAGTATTCGCTTAGATTCCCA ACCTTCGTTTTATTCTTTCGTAGACAAAGAAGCTGCATGCGAACA TAGGGACAACTTTTATAAATCCAATTGTCAAACCAACGTAAAAC CCTCTGGCACCATTTTCAACATATATTTGTGAAGCAGTACGCAAT ATCGATAAATACTCACCGTTGTTTGTAACAGCCCCAACTTGCATA CGCCTTCTAATGACCTCAAATGGATAAGCCGCAGCTTGTGCTAAC ATACCAGCAGCACCGCCCGCGGTCAGCTGCGCCCACACATATAA AGGCAATCTACGATCATGGGAGGAATTAGTTTTGACCGTCAGGT CTTCAAGAGTTTTGAACTCTTCTTCTTGAACTGTGTAACCTTTTAA ATGACGGGATCTAAATACGTCATGGATGAGATCATGTGTGTAAA AACTGACTCCAGCATATGGAATCATTCCAAAGATTGTAGGAGCG AACCCACGATAAAAGTTTCCCAACCTTGCCAAAGTGTCTAATGCT GTGACTTGAAATCTGGGTTCCTCGTTGAAGACCCTGCGTACTATG CCCAAAAACTTTCCTCCACGAGCCCTATTAACTTCTCTATGAGTT TCAAATGCCAAACGGACACGGATTAGGTCCAATGGGTAAGTGAA AAACACAGAGCAAACCCCAGCTAATGAGCCGGCCAGTAACCGTC TTGGAGCTGTTTCATAAGAGTCATTAGGGATCAATAACGTTCTAA TCTGTTCATAACATACAAATTTTATGGCTGCATAGGGAAAAATTC TCAACAGGGTAGCCGAATGACCCTGATATAGACCTGCGACACCA TCATACCCATAGATCTGCCTGACAGCCTTAAAGAGCCCGCTAAA AGACCCGGAAAACCGAGAGAACTCTGGATTAGCAGTCTGAAAAA GAATCTTCACTCTGTCTAGTGGAGCAATTAATGTCTTAGCGGCAC TTCCTGCTACTCCGCCAGCTACTCCTGAATAGATCACATACTGCA AAGACTGCTTGTCGATGACCTTGGGGTTATTTAGCTTCAAGGGCA ATTTTTGGGACATTTTGGACACAGGAGACTCAGAAACAGACACA GAGCGTTCTGAGTCCTGGTGCTCCTGACGTAGGCCTAGAACAGG AATTATTGGCTTTATTTGTTTGTCCATTTCATAGGCTTGGGGTAAT AGATAGATGACAGAGAAATAGAGAAGACCTAATATTTTTTGTTC ATGGCAAATCGCGGGTTCGCGGTCGGGTCACACACGGAGAAGTA ATGAGAAGAGCTGGTAATCTGGGGTAAAAGGGTTCAAAAGAAG GTCGCCTGGTAGGGATGCAATACAAGGTTGTCTTGGAGTTTACAT TGACCAGATGATTTGGCTTTTTCTCTGTTCAATTCACATTTTTCAG CGAGAATCGGATTGACGGAGAAATGGCGGGGTGTGGGGTGGAT AGATGGCAGAAATGCTCGCAATCACCGCGAAAGAAAGACTTTAT GGAATAGAACTACTGGGTGGTGTAAGGATTACATAGCTAGTCCA ATGGAGTCCGTTGGAAAGGTAAGAAGAAGCTAAAACCGGCTAA GTAACTAGGGAAGAATGATCAGACTTTGATTTGATGAGGTCTGA AAATACTCTGCTGCTTTTTCAGTTGCTTTTTCCCTGCAACCTATCA TTTTCCTTTTCATAAGCCTGCCTTTTCTGTTTTCACTTATATGAGTT CCGCCGAGACTTCCCCAAATTCTCTCCTGGAACATTCTCTATCGC TCTCCTTCCAAGTTGCGCCCCCTGGCACTGCCTAGTAATATTACC ACGCGACTTATATTCAGTTCCACAATTTCCAGTGTTCGTAGCAAA TATCATCAGCCATGGCGAAGGCAGATGGCAGTTTGCTCTACTATA ATCCTCACAATCCACCCAGAAGGTATTACTTCTACATGGCTATAT TCGCCGTTTCTGTCATTTGCGTTTTGTACGGACCCTCACAACAATT ATCATCTCCAAAAATAGACTATGATCCATTGACGCTCCGATCACT TGATTTGAAGACTTTGGAAGCTCCTTCACAGTTGAGTCCAGGCAC CGTAGAAGATAATCTTCG 65 Sequence AAAGCTAGAGTAAAATAGATATAGCGAGATTAGAGAATGAATAC of the 3′- CTTCTTCTAAGCGATCGTCCGTCATCATAGAATATCATGGACTGT Region ATAGTTTTTTTTTTGTACATATAATGATTAAACGGTCATCCAACA used for TCTCGTTGACAGATCTCTCAGTACGCGAAATCCCTGACTATCAAA knock out GCAAGAACCGATGAAGAAAAAAACAACAGTAACCCAAACACCA of CAACAAACACTTTATCTTCTCCCCCCCAACACCAATCATCAAAGA PpOCH1: GATGTCGGAACCAAACACCAAGAAGCAAAAACTAACCCCATATA AAAACATCCTGGTAGATAATGCTGGTAACCCGCTCTCCTTCCATA TTCTGGGCTACTTCACGAAGTCTGACCGGTCTCAGTTGATCAACA TGATCCTCGAAATGGGTGGCAAGATCGTTCCAGACCTGCCTCCTC TGGTAGATGGAGTGTTGTTTTTGACAGGGGATTACAAGTCTATTG ATGAAGATACCCTAAAGCAACTGGGGGACGTTCCAATATACAGA GACTCCTTCATCTACCAGTGTTTTGTGCACAAGACATCTCTTCCC ATTGACACTTTCCGAATTGACAAGAACGTCGACTTGGCTCAAGAT TTGATCAATAGGGCCCTTCAAGAGTCTGTGGATCATGTCACTTCT GCCAGCACAGCTGCAGCTGCTGCTGTTGTTGTCGCTACCAACGGC CTGTCTTCTAAACCAGACGCTCGTACTAGCAAAATACAGTTCACT CCCGAAGAAGATCGTTTTATTCTTGACTTTGTTAGGAGAAATCCT AAACGAAGAAACACACATCAACTGTACACTGAGCTCGCTCAGCA CATGAAAAACCATACGAATCATTCTATCCGCCACAGATTTCGTCG TAATCTTTCCGCTCAACTTGATTGGGTTTATGATATCGATCCATTG ACCAACCAACCTCGAAAAGATGAAAACGGGAACTACATCAAGGT ACAAGGCCTTCCA 66 Sequence GGCCGAGCGGGCCTAGATTTTCACTACAAATTTCAAAACTACGC of the 5′- GGATTTATTGTCTCAGAGAGCAATTTGGCATTTCTGAGCGTAGCA Region GGAGGCTTCATAAGATTGTATAGGACCGTACCAACAAATTGCCG used for AGGCACAACACGGTATGCTGTGCACTTATGTGGCTACTTCCCTAC knock out AACGGAATGAAACCTTCCTCTTTCCGCTTAAACGAGAAAGTGTGT of CGCAATTGAATGCAGGTGCCTGTGCGCCTTGGTGTATTGTTTTTG PpBMT2: AGGGCCCAATTTATCAGGCGCCTTTTTTCTTGGTTGTTTTCCCTTA GCCTCAAGCAAGGTTGGTCTATTTCATCTCCGCTTCTATACCGTG CCTGATACTGTTGGATGAGAACACGACTCAACTTCCTGCTGCTCT GTATTGCCAGTGTTTTGTCTGTGATTTGGATCGGAGTCCTCCTTAC TTGGAATGATAATAATCTTGGCGGAATCTCCCTAAACGGAGGCA AGGATTCTGCCTATGATGATCTGCTATCATTGGGAAGCTTCAACG ACATGGAGGTCGACTCCTATGTCACCAACATCTACGACAATGCTC CAGTGCTAGGATGTACGGATTTGTCTTATCATGGATTGTTGAAAG TCACCCCAAAGCATGACTTAGCTTGCGATTTGGAGTTCATAAGAG CTCAGATTTTGGACATTGACGTTTACTCCGCCATAAAAGACTTAG AAGATAAAGCCTTGACTGTAAAACAAAAGGTTGAAAAACACTGG TTTACGTTTTATGGTAGTTCAGTCTTTCTGCCCGAACACGATGTG CATTACCTGGTTAGACGAGTCATCTTTTCGGCTGAAGGAAAGGC GAACTCTCCAGTAACATC 67 Sequence CCATATGATGGGTGTTTGCTCACTCGTATGGATCAAAATTCCATG of the 3′- GTTTCTTCTGTACAACTTGTACACTTATTTGGACTTTTCTAACGGT Region TTTTCTGGTGATTTGAGAAGTCCTTATTTTGGTGTTCGCAGCTTAT used for CCGTGATTGAACCATCAGAAATACTGCAGCTCGTTATCTAGTTTC knock out AGAATGTGTTGTAGAATACAATCAATTCTGAGTCTAGTTTGGGTG of GGTCTTGGCGACGGGACCGTTATATGCATCTATGCAGTGTTAAGG PpBMT2: TACATAGAATGAAAATGTAGGGGTTAATCGAAAGCATCGTTAAT TTCAGTAGAACGTAGTTCTATTCCCTACCCAAATAATTTGCCAAG AATGCTTCGTATCCACATACGCAGTGGACGTAGCAAATTTCACTT TGGACTGTGACCTCAAGTCGTTATCTTCTACTTGGACATTGATGG TCATTACGTAATCCACAAAGAATTGGATAGCCTCTCGTTTTATCT AGTGCACAGCCTAATAGCACTTAAGTAAGAGCAATGGACAAATT TGCATAGACATTGAGCTAGATACGTAACTCAGATCTTGTTCACTC ATGGTGTACTCGAAGTACTGCTGGAACCGTTACCTCTTATCATTT CGCTACTGGCTCGTGAAACTACTGGATGAAAAAAAAAAAAGAGC TGAAAGCGAGATCATCCCATTTTGTCATCATACAAATTCACGCTT GCAGTTTTGCTTCGTTAACAAGACAAGATGTCTTTATCAAAGACC CGTTTTTTCTTCTTGAAGAATACTTCCCTGTTGAGCACATGCAAA CCATATTTATCTCAGATTTCACTCAACTTGGGTGCTTCCAAGAGA AGTAAAATTCTTCCCACTGCATCAACTTCCAAGAAACCCGTAGAC CAGTTTCTCTTCAGCCAAAAGAAGTTGCTCGCCGATCACCGCGGT AACAGAGGAGTCAGAAGGTTTCACACCCTTCCATCCCGATTTCA AAGTCAAAGTGCTGCGTTGAACCAAGGTTTTCAGGTTGCCAAAG CCCAGTCTGCAAAAACTAGTTCCAAATGGCCTATTAATTCCCATA AAAGTGTTGGCTACGTATGTATCGGTACCTCCATTCTGGTATTTG CTATTGTTGTCGTTGGTGGGTTGACTAGACTGACCGAATCCGGTC TTTCCATAACGGAGTGGAAACCTATCACTGGTTCGGTTCCCCCAC TGACTGAGGAAGACTGGAAGTTGGAATTTGAAAAATACAAACAA AGCCCTGAGTTTCAGGAACTAAATTCTCACATAACATTGGAAGA GTTCAAGTTTATATTTTCCATGGAATGGGGACATAGATTGTTGGG AAGGGTCATCGGCCTGTCGTTTGTTCTTCCCACGTTTTACTTCATT GCCCGTCGAAAGTGTTCCAAAGATGTTGCATTGAAACTGCTTGCA ATATGCTCTATGATAGGATTCCAAGGTTTCATCGGCTGGTGGATG GTGTATTCCGGATTGGACAAACAGCAATTGGCTGAACGTAACTC CAAACCAACTGTGTCTCCATATCGCTTAACTACCCATCTTGGAAC TGCATTTGTTATTTACTGTTACATGATTTACACAGGGCTTCAAGTT TTGAAGAACTATAAGATCATGAAACAGCCTGAAGCGTATGTTCA AATTTTCAAGCAAATTGCGTCTCCAAAATTGAAAACTTTCAAGAG ACTCTCTTCAGTTCTATTAGGCCTGGTG 68 Sequence CATATGGTGAGAGCCGTTCTGCACAACTAGATGTTTTCGAGCTTC of the 5′- GCATTGTTTCCTGCAGCTCGACTATTGAATTAAGATTTCCGGATA Region TCTCCAATCTCACAAAAACTTATGTTGACCACGTGCTTTCCTGAG used for GCGAGGTGTTTTATATGCAAGCTGCCAAAAATGGAAAACGAATG knock out GCCATTTTTCGCCCAGGCAAATTATTCGATTACTGCTGTCATAAA of BMT1 GACAGTGTTGCAAGGCTCACATTTTTTTTTAGGATCCGAGATAAA GTGAATACAGGACAGCTTATCTCTATATCTTGTACCATTCGTGAA TCTTAAGAGTTCGGTTAGGGGGACTCTAGTTGAGGGTTGGCACTC ACGTATGGCTGGGCGCAGAAATAAAATTCAGGCGCAGCAGCACT TATCGATG 69 Sequence GAATTCACAGTTATAAATAAAAACAAAAACTCAAAAAGTTTGGG of the 3′- CTCCACAAAATAACTTAATTTAAATTTTTGTCTAATAAATGAATG Region TAATTCCAAGATTATGTGATGCAAGCACAGTATGCTTCAGCCCTA used for TGCAGCTACTAATGTCAATCTCGCCTGCGAGCGGGCCTAGATTTT knock out CACTACAAATTTCAAAACTACGCGGATTTATTGTCTCAGAGAGCA of BMT1 ATTTGGCATTTCTGAGCGTAGCAGGAGGCTTCATAAGATTGTATA GGACCGTACCAACAAATTGCCGAGGCACAACACGGTATGCTGTG CACTTATGTGGCTACTTCCCTACAACGGAATGAAACCTTCCTCTT TCCGCTTAAACGAGAAAGTGTGTCGCAATTGAATGCAGGTGCCT GTGCGCCTTGGTGTATTGTTTTTGAGGGCCCAATTTATCAGGCGC CTTTTTTCTTGGTTGTTTTCCCTTAGCCTCAAGCAAGGTTGGTCTA TTTCATCTCCGCTTCTATACCGTGCCTGATACTGTTGGATGAGAA CACGACTCAACTTCCTGCTGCTCTGTATTGCCAGTGTTTTGTCTGT GATTTGGATCGGAGTCCTCCTTACTTGGAATGATAATAATCTTGG CGGAATCTCCCTAAACGGAGGCAAGGATTCTGCCTATGATGATC TGCTATCATTGGGAAGCTT 70 Sequence GATATCTCCCTGGGGACAATATGTGTTGCAACTGTTCGTTGTTGG of the 5′- TGCCCCAGTCCCCCAACCGGTACTAATCGGTCTATGTTCCCGTAA Region CTCATATTCGGTTAGAACTAGAACAATAAGTGCATCATTGTTCAA used for CATTGTGGTTCAATTGTCGAACATTGCTGGTGCTTATATCTACAG knock out GGAAGACGATAAGCCTTTGTACAAGAGAGGTAACAGACAGTTAA of BMT3 TTGGTATTTCTTTGGGAGTCGTTGCCCTCTACGTTGTCTCCAAGAC ATACTACATTCTGAGAAACAGATGGAAGACTCAAAAATGGGAGA AGCTTAGTGAAGAAGAGAAAGTTGCCTACTTGGACAGAGCTGAG AAGGAGAACCTGGGTTCTAAGAGGCTGGACTTTTTGTTCGAGAG TTAAACTGCATAATTTTTTCTAAGTAAATTTCATAGTTATGAAAT TTCTGCAGCTTAGTGTTTACTGCATCGTTTACTGCATCACCCTGTA AATAATGTGAGCTTTTTTCCTTCCATTGCTTGGTATCTTCCTTGCT GCTGTTT 71 Sequence ACAAAACAGTCATGTACAGAACTAACGCCTTTAAGATGCAGACC of the 3′- ACTGAAAAGAATTGGGTCCCATTTTTCTTGAAAGACGACCAGGA Region ATCTGTCCATTTTGTTTACTCGTTCAATCCTCTGAGAGTACTCAAC used for TGCAGTCTTGATAACGGTGCATGTGATGTTCTATTTGAGTTACCA knock out CATGATTTTGGCATGTCTTCCGAGCTACGTGGTGCCACTCCTATG of BMT3 CTCAATCTTCCTCAGGCAATCCCGATGGCAGACGACAAAGAAAT TTGGGTTTCATTCCCAAGAACGAGAATATCAGATTGCGGGTGTTC TGAAACAATGTACAGGCCAATGTTAATGCTTTTTGTTAGAGAAG GAACAAACTTTTTTGCTGAGC 72 Sequence AAGCTTGTTCACCGTTGGGACTTTTCCGTGGACAATGTTGACTAC of the 5′- TCCAGGAGGGATTCCAGCTTTCTCTACTAGCTCAGCAATAATCAA Region TGCAGCCCCAGGCGCCCGTTCTGATGGCTTGATGACCGTTGTATT used for GCCTGTCACTATAGCCAGGGGTAGGGTCCATAAAGGAATCATAG knock out CAGGGAAATTAAAAGGGCATATTGATGCAATCACTCCCAATGGC of BMT4 TCTCTTGCCATTGAAGTCTCCATATCAGCACTAACTTCCAAGAAG GACCCCTTCAAGTCTGACGTGATAGAGCACGCTTGCTCTGCCACC TGTAGTCCTCTCAAAACGTCACCTTGTGCATCAGCAAAGACTTTA CCTTGCTCCAATACTATGACGGAGGCAATTCTGTCAAAATTCTCT CTCAGCAATTCAACCAACTTGAAAGCAAATTGCTGTCTCTTGATG ATGGAGACTTTTTTCCAAGATTGAAATGCAATGTGGGACGACTC AATTGCTTCTTCCAGCTCCTCTTCGGTTGATTGAGGAACTTTTGA AACCACAAAATTGGTCGTTGGGTCATGTACATCAAACCATTCTGT AGATTTAGATTCGACGAAAGCGTTGTTGATGAAGGAAAAGGTTG GATACGGTTTGTCGGTCTCTTTGGTATGGCCGGTGGGGTATGCAA TTGCAGTAGAAGATAATTGGACAGCCATTGTTGAAGGTAGAGAA AAGGTCAGGGAACTTGGGGGTTATTTATACCATTTTACCCCACAA ATAACAACTGAAAAGTACCCATTCCATAGTGAGAGGTAACCGAC GGAAAAAGACGGGCCCATGTTCTGGGACCAATAGAACTGTGTAA TCCATTGGGACTAATCAACAGACGATTGGCAATATAATGAAATA GTTCGTTGAAAAGCCACGTCAGCTGTCTTTTCATTAACTTTGGTC GGACACAACATTTTCTACTGTTGTATCTGTCCTACTTTGCTTATCA TCTGCCACAGGGCAAGTGGATTTCCTTCTCGCGCGGCTGGGTGAA AACGGTTAACGTGAA 73 Sequence GCCTTGGGGGACTTCAAGTCTTTGCTAGAAACTAGATGAGGTCA of the 3′- GGCCCTCTTATGGTTGTGTCCCAATTGGGCAATTTCACTCACCTA Region AAAAGCATGACAATTATTTAGCGAAATAGGTAGTATATTTTCCCT used for CATCTCCCAAGCAGTTTCGTTTTTGCATCCATATCTCTCAAATGA knock out GCAGCTACGACTCATTAGAACCAGAGTCAAGTAGGGGTGAGCTC of BMT4 AGTCATCAGCCTTCGTTTCTAAAACGATTGAGTTCTTTTGTTGCTA CAGGAAGCGCCCTAGGGAACTTTCGCACTTTGGAAATAGATTTT GATGACCAAGAGCGGGAGTTGATATTAGAGAGGCTGTCCAAAGT ACATGGGATCAGGCCGGCCAAATTGATTGGTGTGACTAAACCAT TGTGTACTTGGACACTCTATTACAAAAGCGAAGATGATTTGAAGT ATTACAAGTCCCGAAGTGTTAGAGGATTCTATCGAGCCCAGAAT GAAATCATCAACCGTTATCAGCAGATTGATAAACTCTTGGAAAG CGGTATCCCATTTTCATTATTGAAGAACTACGATAATGAAGATGT GAGAGACGGCGACCCTCTGAACGTAGACGAAGAAACAAATCTAC TTTTGGGGTACAATAGAGAAAGTGAATCAAGGGAGGTATTTGTG GCCATAATACTCAACTCTATCATTAATG 74 Sequence TCATTCTATATGTTCAAGAAAAGGGTAGTGAAAGGAAAGAAAAG of the 5′- GCATATAGGCGAGGGAGAGTTAGCTAGCATACAAGATAATGAAG Region GATCAATAGCGGTAGTTAAAGTGCACAAGAAAAGAGCACCTGTT used for GAGGCTGATGATAAAGCTCCAATTACATTGCCACAGAGAAACAC knock out AGTAACAGAAATAGGAGGGGATGCACCACGAGAAGAGCATTCA of PpPNO1 GTGAACAACTTTGCCAAATTCATAACCCCAAGCGCTAATAAGCC and AATGTCAAAGTCGGCTACTAACATTAATAGTACAACAACTATCG PpMNN4: ATTTTCAACCAGATGTTTGCAAGGACTACAAACAGACAGGTTAC TGCGGATATGGTGACACTTGTAAGTTTTTGCACCTGAGGGATGAT TTCAAACAGGGATGGAAATTAGATAGGGAGTGGGAAAATGTCCA AAAGAAGAAGCATAATACTCTCAAAGGGGTTAAGGAGATCCAA ATGTTTAATGAAGATGAGCTCAAAGATATCCCGTTTAAATGCATT ATATGCAAAGGAGATTACAAATCACCCGTGAAAACTTCTTGCAA TCATTATTTTTGCGAACAATGTTTCCTGCAACGGTCAAGAAGAAA ACCAAATTGTATTATATGTGGCAGAGACACTTTAGGAGTTGCTTT ACCAGCAAAGAAGTTGTCCCAATTTCTGGCTAAGATACATAATA ATGAAAGTAATAAAGTTTAGTAATTGCATTGCGTTGACTATTGAT TGCATTGATGTCGTGTGATACTTTCACCGAAAAAAAACACGAAG CGCAATAGGAGCGGTTGCATATTAGTCCCCAAAGCTATTTAATTG TGCCTGAAACTGTTTTTTAAGCTCATCAAGCATAATTGTATGCAT TGCGACGTAACCAACGTTTAGGCGCAGTTTAATCATAGCCCACTG CTAAGCC 75 Sequence CGGAGGAATGCAAATAATAATCTCCTTAATTACCCACTGATAAG of the 3′- CTCAAGAGACGCGGTTTGAAAACGATATAATGAATCATTTGGAT Region TTTATAATAAACCCTGACAGTTTTTCCACTGTATTGTTTTAACACT used for CATTGGAAGCTGTATTGATTCTAAGAAGCTAGAAATCAATACGG knock out CCATACAAAAGATGACATTGAATAAGCACCGGCTTTTTTGATTAG of PpPNO1 CATATACCTTAAAGCATGCATTCATGGCTACATAGTTGTTAAAGG and GCTTCTTCCATTATCAGTATAATGAATTACATAATCATGCACTTA PpMNN4: TATTTGCCCATCTCTGTTCTCTCACTCTTGCCTGGGTATATTCTAT GAAATTGCGTATAGCGTGTCTCCAGTTGAACCCCAAGCTTGGCG AGTTTGAAGAGAATGCTAACCTTGCGTATTCCTTGCTTCAGGAAA CATTCAAGGAGAAACAGGTCAAGAAGCCAAACATTTTGATCCTT CCCGAGTTAGCATTGACTGGCTACAATTTTCAAAGCCAGCAGCG GATAGAGCCTTTTTTGGAGGAAACAACCAAGGGAGCTAGTACCC AATGGGCTCAAAAAGTATCCAAGACGTGGGATTGCTTTACTTTA ATAGGATACCCAGAAAAAAGTTTAGAGAGCCCTCCCCGTATTTA CAACAGTGCGGTACTTGTATCGCCTCAGGGAAAAGTAATGAACA ACTACAGAAAGTCCTTCTTGTATGAAGCTGATGAACATTGGGGA TGTTCGGAATCTTCTGATGGGTTTCAAACAGTAGATTTATTAATT GAAGGAAAGACTGTAAAGACATCATTTGGAATTTGCATGGATTT GAATCCTTATAAATTTGAAGCTCCATTCACAGACTTCGAGTTCAG TGGCCATTGCTTGAAAACCGGTACAAGACTCATTTTGTGCCCAAT GGCCTGGTTGTCCCCTCTATCGCCTTCCATTAAAAAGGATCTTAG TGATATAGAGAAAAGCAGACTTCAAAAGTTCTACCTTGAAAAAA TAGATACCCCGGAATTTGACGTTAATTACGAATTGAAAAAAGAT GAAGTATTGCCCACCCGTATGAATGAAACGTTGGAAACAATTGA CTTTGAGCCTTCAAAACCGGACTACTCTAATATAAATTATTGGAT ACTAAGGTTTTTTCCCTTTCTGACTCATGTCTATAAACGAGATGT GCTCAAAGAGAATGCAGTTGCAGTCTTATGCAACCGAGTTGGCA TTGAGAGTGATGTCTTGTACGGAGGATCAACCACGATTCTAAACT TCAATGGTAAGTTAGCATCGACACAAGAGGAGCTGGAGTTGTAC GGGCAGACTAATAGTCTCAACCCCAGTGTGGAAGTATTGGGGGC CCTTGGCATGGGTCAACAGGGAATTCTAGTACGAGACATTGAAT TAACATAATATACAATATACAATAAACACAAATAAAGAATACAA GCCTGACAAAAATTCACAAATTATTGCCTAGACTTGTCGTTATCA GCAGCGACCTTTTTCCAATGCTCAATTTCACGATATGCCTTTTCTA GCTCTGCTTTAAGCTTCTCATTGGAATTGGCTAACTCGTTGACTG CTTGGTCAGTGATGAGTTTCTCCAAGGTCCATTTCTCGATGTTGTT GTTTTCGTTTTCCTTTAATCTCTTGATATAATCAACAGCCTTCTTT AATATCTGAGCCTTGTTCGAGTCCCCTGTTGGCAACAGAGCGGCC AGTTCCTTTATTCCGTGGTTTATATTTTCTCTTCTACGCCTTTCTAC TTCTTTGTGATTCTCTTTACGCATCTTATGCCATTCTTCAGAACCA GTGGCTGGCTTAACCGAATAGCCAGAGCCTGAAGAAGCCGCACT AGAAGAAGCAGTGGCATTGTTGACTATGG 76 Sequence GATCTGGCCATTGTGAAACTTGACACTAAAGACAAAACTCTTAG of the 5′- AGTTTCCAATCACTTAGGAGACGATGTTTCCTACAACGAGTACGA Region TCCCTCATTGATCATGAGCAATTTGTATGTGAAAAAAGTCATCGA used for CCTTGACACCTTGGATAAAAGGGCTGGAGGAGGTGGAACCACCT knock out GTGCAGGCGGTCTGAAAGTGTTCAAGTACGGATCTACTACCAAA of TATACATCTGGTAACCTGAACGGCGTCAGGTTAGTATACTGGAA PpMNN4L1: CGAAGGAAAGTTGCAAAGCTCCAAATTTGTGGTTCGATCCTCTA ATTACTCTCAAAAGCTTGGAGGAAACAGCAACGCCGAATCAATT GACAACAATGGTGTGGGTTTTGCCTCAGCTGGAGACTCAGGCGC ATGGATTCTTTCCAAGCTACAAGATGTTAGGGAGTACCAGTCATT CACTGAAAAGCTAGGTGAAGCTACGATGAGCATTTTCGATTTCC ACGGTCTTAAACAGGAGACTTCTACTACAGGGCTTGGGGTAGTT GGTATGATTCATTCTTACGACGGTGAGTTCAAACAGTTTGGTTTG TTCACTCCAATGACATCTATTCTACAAAGACTTCAACGAGTGACC AATGTAGAATGGTGTGTAGCGGGTTGCGAAGATGGGGATGTGGA CACTGAAGGAGAACACGAATTGAGTGATTTGGAACAACTGCATA TGCATAGTGATTCCGACTAGTCAGGCAAGAGAGAGCCCTCAAAT TTACCTCTCTGCCCCTCCTCACTCCTTTTGGTACGCATAATTGCAG TATAAAGAACTTGCTGCCAGCCAGTAATCTTATTTCATACGCAGT TCTATATAGCACATAATCTTGCTTGTATGTATGAAATTTACCGCG TTTTAGTTGAAATTGTTTATGTTGTGTGCCTTGCATGAAATCTCTC GTTAGCCCTATCCTTACATTTAACTGGTCTCAAAACCTCTACCAA TTCCATTGCTGTACAACAATATGAGGCGGCATTACTGTAGGGTTG GAAAAAAATTGTCATTCCAGCTAGAGATCACACGACTTCATCAC GCTTATTGCTCCTCATTGCTAAATCATTTACTCTTGACTTCGACCC AGAAAAGTTCGCC 77 Sequence GCATGTCAAACTTGAACACAACGACTAGATAGTTGTTTTTTCTAT of the 3′- ATAAAACGAAACGTTATCATCTTTAATAATCATTGAGGTTTACCC Region TTATAGTTCCGTATTTTCGTTTCCAAACTTAGTAATCTTTTGGAAA used for TATCATCAAAGCTGGTGCCAATCTTCTTGTTTGAAGTTTCAAACT knock out GCTCCACCAAGCTACTTAGAGACTGTTCTAGGTCTGAAGCAACTT of CGAACACAGAGACAGCTGCCGCCGATTGTTCTTTTTTGTGTTTTT PpMNN4L1: CTTCTGGAAGAGGGGCATCATCTTGTATGTCCAATGCCCGTATCC TTTCTGAGTTGTCCGACACATTGTCCTTCGAAGAGTTTCCTGACA TTGGGCTTCTTCTATCCGTGTATTAATTTTGGGTTAAGTTCCTCGT TTGCATAGCAGTGGATACCTCGATTTTTTTGGCTCCTATTTACCTG ACATAATATTCTACTATAATCCAACTTGGACGCGTCATCTATGAT AACTAGGCTCTCCTTTGTTCAAAGGGGACGTCTTCATAATCCACT GGCACGAAGTAAGTCTGCAACGAGGCGGCTTTTGCAACAGAACG ATAGTGTCGTTTCGTACTTGGACTATGCTAAACAAAAGGATCTGT CAAACATTTCAACCGTGTTTCAAGGCACTCTTTACGAATTATCGA CCAAGACCTTCCTAGACGAACATTTCAACATATCCAGGCTACTGC TTCAAGGTGGTGCAAATGATAAAGGTATAGATATTAGATGTGTTT GGGACCTAAAACAGTTCTTGCCTGAAGATTCCCTTGAGCAACAG GCTTCAATAGCCAAGTTAGAGAAGCAGTACCAAATCGGTAACAA AAGGGGGAAGCATATAAAACCTTTACTATTGCGACAAAATCCAT CCTTGAAAGTAAAGCTGTTTGTTCAATGTAAAGCATACGAAACG AAGGAGGTAGATCCTAAGATGGTTAGAGAACTTAACGGGACATA CTCCAGCTGCATCCCATATTACGATCGCTGGAAGACTTTTTTCAT GTACGTATCGCCCACCAACCTTTCAAAGCAAGCTAGGTATGATTT TGACAGTTCTCACAATCCATTGGTTTTCATGCAACTTGAAAAAAC CCAACTCAAACTTCATGGGGATCCATACAATGTAAATCATTACG AGAGGGCGAGGTTGAAAAGTTTCCATTGCAATCACGTCGCATCA TGGCTACTGAAAGGCCTTAAC 78 Sequence TAATGGCCAAACGGTTTCTCAATTACTATATACTACTAACCATTT of the ACCTGTAGCGTATTTCTTTTCCCTCTTCGCGAAAGCTCAAGGGCA PpTRP2 TCTTCTTGACTCATGAAAAATATCTGGATTTCTTCTGACAGATCA gene TCACCCTTGAGCCCAACTCTCTAGCCTATGAGTGTAAGTGATAGT integration CATCTTGCAACAGATTATTTTGGAACGCAACTAACAAAGCAGAT locus: ACACCCTTCAGCAGAATCCTTTCTGGATATTGTGAAGAATGATCG CCAAAGTCACAGTCCTGAGACAGTTCCTAATCTTTACCCCATTTA CAAGTTCATCCAATCAGACTTCTTAACGCCTCATCTGGCTTATAT CAAGCTTACCAACAGTTCAGAAACTCCCAGTCCAAGTTTCTTGCT TGAAAGTGCGAAGAATGGTGACACCGTTGACAGGTACACCTTTA TGGGACATTCCCCCAGAAAAATAATCAAGACTGGGCCTTTAGAG GGTGCTGAAGTTGACCCCTTGGTGCTTCTGGAAAAAGAACTGAA GGGCACCAGACAAGCGCAACTTCCTGGTATTCCTCGTCTAAGTG GTGGTGCCATAGGATACATCTCGTACGATTGTATTAAGTACTTTG AACCAAAAACTGAAAGAAAACTGAAAGATGTTTTGCAACTTCCG GAAGCAGCTTTGATGTTGTTCGACACGATCGTGGCTTTTGACAAT GTTTATCAAAGATTCCAGGTAATTGGAAACGTTTCTCTATCCGTT GATGACTCGGACGAAGCTATTCTTGAGAAATATTATAAGACAAG AGAAGAAGTGGAAAAGATCAGTAAAGTGGTATTTGACAATAAA ACTGTTCCCTACTATGAACAGAAAGATATTATTCAAGGCCAAAC GTTCACCTCTAATATTGGTCAGGAAGGGTATGAAAACCATGTTCG CAAGCTGAAAGAACATATTCTGAAAGGAGACATCTTCCAAGCTG TTCCCTCTCAAAGGGTAGCCAGGCCGACCTCATTGCACCCTTTCA ACATCTATCGTCATTTGAGAACTGTCAATCCTTCTCCATACATGT TCTATATTGACTATCTAGACTTCCAAGTTGTTGGTGCTTCACCTG AATTACTAGTTAAATCCGACAACAACAACAAAATCATCACACAT CCTATTGCTGGAACTCTTCCCAGAGGTAAAACTATCGAAGAGGA CGACAATTATGCTAAGCAATTGAAGTCGTCTTTGAAAGACAGGG CCGAGCACGTCATGCTGGTAGATTTGGCCAGAAATGATATTAAC CGTGTGTGTGAGCCCACCAGTACCACGGTTGATCGTTTATTGACT GTGGAGAGATTTTCTCATGTGATGCATCTTGTGTCAGAAGTCAGT GGAACATTGAGACCAAACAAGACTCGCTTCGATGCTTTCAGATC CATTTTCCCAGCAGGAACCGTCTCCGGTGCTCCGAAGGTAAGAG CAATGCAACTCATAGGAGAATTGGAAGGAGAAAAGAGAGGTGT TTATGCGGGGGCCGTAGGACACTGGTCGTACGATGGAAAATCGA TGGACACATGTATTGCCTTAAGAACAATGGTCGTCAAGGACGGT GTCGCTTACCTTCAAGCCGGAGGTGGAATTGTCTACGATTCTGAC CCCTATGACGAGTACATCGAAACCATGAACAAAATGAGATCCAA CAATAACACCATCTTGGAGGCTGAGAAAATCTGGACCGATAGGT TGGCCAGAGACGAGAATCAAAGTGAATCCGAAGAAAACGATCA ATGAACGGAGGACGTAAGTAGGAATTTATGGTTTGGCCAT 79 Sequence GATCTGGCCTTCCCTGAATTTTTACGTCCAGCTATACGATCCGTT of the 5′- GTGACTGTATTTCCTGAAATGAAGTTTCAACCTAAAGTTTTGGTT Region GTACTTGCTCCACCTACCACGGAAACTAATATCGAAACCAATGA used for AAAAGTAGAACTGGAATCGTCAATCGAAATTCGCAACCAAGTGG knock out AACCCAAAGACTTGAATCTTTCTAAAGTCTATTCTAGTGACACTA of ATGGCAACAGAAGATTTGAGCTGACTTTTCAAATGAATCTCAAT PpARG1: AATGCAATATCAACATCAGACAATCAATGGGCTTTGTCTAGTGA CACAGGATCAATTATAGTAGTGTCTTCTGCAGGAAGAATAACTTC CCCGATCCTAGAAGTCGGGGCATCCGTCTGTGTCTTAAGATCGTA CAACGAACACCTTTTGGCAATAACTTGTGAAGGAACATGCTTTTC ATGGAATTTAAAGAAGCAAGAATGTGTTCTAAACAGCATTTCAT TAGCACCTATAGTCAATTCACACATGCTAGTTAAGAAAGTTGGA GATGCAAGGAACTATTCTATTGTATCTGCCGAAGGAGACAACAA TCCGTTACCCCAGATTCTAGACTGCGAACTTTCCAAAAATGGCGC TCCAATTGTGGCTCTTAGCACGAAAGACATCTACTCTTATTCAAA GAAAATGAAATGCTGGATCCATTTGATTGATTCGAAATACTTTGA ATTGTTGGGTGCTGACAATGCACTGTTTGAGTGTGTGGAAGCGCT AGAAGGTCCAATTGGAATGCTAATTCATAGATTGGTAGATGAGT TCTTCCATGAAAACACTGCCGGTAAAAAACTCAAACTTTACAAC AAGCGAGTACTGGAGGACCTTTCAAATTCACTTGAAGAACTAGG TGAAAATGCGTCTCAATTAAGAGAGAAACTTGACAAACTCTATG GTGATGAGGTTGAGGCTTCTTGACCTCTTCTCTCTATCTGCGTTTC TTTTTTTTTTTTTTTTTTTTTTTTTTTCAGTTGAGCCAGACCGCGCT AAACGCATACCAATTGCCAAATCAGGCAATTGTGAGACAGTGGT AAAAAAGATGCCTGCAAAGTTAGATTCACACAGTAAGAGAGATC CTACTCATAAATGAGGCGCTTATTTAGTAGCTAGTGATAGCCACT GCGGTTCTGCTTTATGCTATTTGTTGTATGCCTTACTATCTTTGTT TGGCTCCTTTTTCTTGACGTTTTCCGTTGGAGGGACTCCCTATTCT GAGTCATGAGCCGCACAGATTATCGCCCAAAATTGACAAAATCT TCTGGCGAAAAAAGTATAAAAGGAGAAAAAAGCTCACCCTTTTC CAGCGTAGAAAGTATATATCAGTCATTGAAGAC 80 Sequence GGGACTTTAACTCAAGTAAAAGGATAGTTGTACAATTATATATA of the 3′- CGAAGAATAAATCATTACAAAAAGTATTCGTTTCTTTGATTCTTA Region ACAGGATTCATTTTCTGGGTGTCATCAGGTACAGCGCTGAATATC used for TTGAAGTTAACATCGAGCTCATCATCGACGTTCATCACACTAGCC knock out ACGTTTCCGCAACGGTAGCAATAATTAGGAGCGGACCACACAGT of GACGACATCTTTCTCTTTGAAATGGTATCTGAAGCCTTCCATGAC PpARG1: CAATTGATGGGCTCTAGCGATGAGTTGCAAGTTATTAATGTGGTT GAACTCACGTGCTACTCGAGCACCGAATAACCAGCCAGCTCCAC GAGGAGAAACAGCCCAACTGTCGACTTCATCTGGGTCAGACCAA ACCAAGTCACAAAATCCTCCTTCATGAGGGACCTCTTGCGCTCGG CTGAGAACTCTGATTTGATCTAACATGCGAATATCGGGAGAGAG ACCACCATGGATACATAATATTTTACCATCAATGATGGCACTAAG GGTTAAAAAGTCGAACACCTGGCAACAGTACTTCCAGACAGTGG TGGAACCATATTTATTGAGACATTCCTCATAAAATCCATAAACCT GAGTGATCTGTCTGGATTCATGATTTCCCCTTACCAATGTGATAT GTTGAGGAAACTTAATTTTTAAAATCATGAGTAACGTGAACGTCT CCAACGAGAAATAGCCTCTATCCACATAGTCTCCTAGGAAGATA TAGTTCTGTTTTATTCCATTAGAGGAGGATCCGGGAAACCCACCA CTAATCTTGAAAAGTTCCAGTAGATCGTGAAATTGGCCGTGAAT ATCTCCGCATACTGTCACTGGACTCTGCACTGGCTGTATATTGGA TTCCTCCATCAGCAAATCCTTCACCCGTTCGCAAAGATGCTTCAT ATCATTTTCACTTAAAGCCTTGCAGCTTTTGACTTCTTCAAACCAC TGATCTGGTCCTCTTTCTGGCATGATTAAGGTCTATAATATTTCTG AGCTGAGATGTAAAAAAAAATAATAAAAATGGGGAGTGAAAAA GTGTGTAGCTTTTAGGAGTTTGGGATTGATACCCCAAAATGATCT TTATGAGAATTAAAAGGTAGATACGCTTTTAATAAGAACACCTA TCTATAGTACTTTGTGGTCTTGAGTAATTGAGATGTTCAGCTTCT GAGGTTTGCCGTTATTCTGGGATAGTAGTGCGCGACCAAACAAC CCGCCAGGCAAAGTGTGTTGTGCTCGAAGACGATTGCCAGAAGA GTAAGTCCGTCCTGCCTCAGATGTTACACACTTTCTTCCCTAGAC AGTCGATGCATCATCGGATTTAAACCTGAAACTTTGATGCCATGA TACGCCTAGTCACGTCGACTGAGATTTTAGATAAGCCCCGATCCC TTTAGTACATTCCTGTTATCCATGGATGGAATGGCCTGATA 81 Sequence CAGTTGAGCCAGACCGCGCTAAACGCATACCAATTGCCAAATCA of the GGCAATTGTGAGACAGTGGTAAAAAAGATGCCTGCAAAGTTAGA PpARG1 TTCACACAGTAAGAGAGATCCTACTCATAAATGAGGCGCTTATTT auxotrophic AGTAGCTAGTGATAGCCACTGCGGTTCTGCTTTATGCTATTTGTT marker: GTATGCCTTACTATCTTTGTTTGGCTCCTTTTTCTTGACGTTTTCC GTTGGAGGGACTCCCTATTCTGAGTCATGAGCCGCACAGATTATC GCCCAAAATTGACAAAATCTTCTGGCGAAAAAAGTATAAAAGGA GAAAAAAGCTCACCCTTTTCCAGCGTAGAAAGTATATATCAGTC ATTGAAGACTATTATTTAAATAACACAATGTCTAAAGGAAAAGT TTGTTTGGCCTACTCCGGTGGTTTGGATACCTCCATCATCCTAGCT TGGTTGTTGGAGCAGGGATACGAAGTCGTTGCCTTTTTAGCCAAC ATTGGTCAAGAGGAAGACTTTGAGGCTGCTAGAGAGAAAGCTCT GAAGATCGGTGCTACCAAGTTTATCGTCAGTGACGTTAGGAAGG AATTTGTTGAGGAAGTTTTGTTCCCAGCAGTCCAAGTTAACGCTA TCTACGAGAACGTCTACTTACTGGGTACCTCTTTGGCCAGACCAG TCATTGCCAAGGCCCAAATAGAGGTTGCTGAACAAGAAGGTTGT TTTGCTGTTGCCCACGGTTGTACCGGAAAGGGTAACGATCAGGTT AGATTTGAGCTTTCCTTTTATGCTCTGAAGCCTGACGTTGTCTGTA TCGCCCCATGGAGAGACCCAGAATTCTTCGAAAGATTCGCTGGT AGAAATGACTTGCTGAATTACGCTGCTGAGAAGGATATTCCAGT TGCTCAGACTAAAGCCAAGCCATGGTCTACTGATGAGAACATGG CTCACATCTCCTTCGAGGCTGGTATTCTAGAAGATCCAAACACTA CTCCTCCAAAGGACATGTGGAAGCTCACTGTTGACCCAGAAGAT GCACCAGACAAGCCAGAGTTCTTTGACGTCCACTTTGAGAAGGG TAAGCCAGTTAAATTAGTTCTCGAGAACAAAACTGAGGTCACCG ATCCGGTTGAGATCTTTTTGACTGCTAACGCCATTGCTAGAAGAA ACGGTGTTGGTAGAATTGACATTGTCGAGAACAGATTCATCGGA ATCAAGTCCAGAGGTTGTTATGAAACTCCAGGTTTGACTCTACTG AGAACCACTCACATCGACTTGGAAGGTCTTACCGTTGACCGTGA AGTTAGATCGATCAGAGACACTTTTGTTACCCCAACCTACTCTAA GTTGTTATACAACGGGTTGTACTTTACCCCAGAAGGTGAGTACGT CAGAACTATGATTCAGCCTTCTCAAAACACCGTCAACGGTGTTGT TAGAGCCAAGGCCTACAAAGGTAATGTGTATAACCTAGGAAGAT ACTCTGAAACCGAGAAATTGTACGATGCTACCGAATCTTCCATG GATGAGTTGACCGGATTCCACCCTCAAGAAGCTGGAGGATTTAT CACAACACAAGCCATCAGAATCAAGAAGTACGGAGAAAGTGTC AGAGAGAAGGGAAAGTTTTTGGGACTTTAACTCAAGTAAAAGGA TAGTTGTACAATTATATATACGAAGAATAAATCATTACAAAAAG TATTCGTTTCTTTGATTCTTAACAGGATTCATTTTCTGGGTGTCAT CAGGTACAGCGCTGAATATCTTGAAGTTAACATCGAGCTCATCAT CGACGTTCATCACACTAGCCACGTTTCCGCAACGGTAGCAATAAT TAGGAGCGGACCACACAGTGACGACATC 82 Sequence GAGTCGGCCAAGAGATGATAACTGTTACTAAGCTTCTCCGTAATT of the 5′- AGTGGTATTTTGTAACTTTTACCAATAATCGTTTATGAATACGGA region that TATTTTTCGACCTTATCCAGTGCCAAATCACGTAACTTAATCATG was used GTTTAAATACTCCACTTGAACGATTCATTATTCAGAAAAAAGTCA to knock GGTTGGCAGAAACACTTGGGCGCTTTGAAGAGTATAAGAGTATT into the AAGCATTAAACATCTGAACTTTCACCGCCCCAATATACTACTCTA PpADE1 GGAAACTCGAAAAATTCCTTTCCATGTGTCATCGCTTCCAACACA locus: CTTTGCTGTATCCTTCCAAGTATGTCCATTGTGAACACTGATCTG GACGGAATCCTACCTTTAATCGCCAAAGGAAAGGTTAGAGACAT TTATGCAGTCGATGAGAACAACTTGCTGTTCGTCGCAACTGACCG TATCTCCGCTTACGATGTGATTATGACAAACGGTATTCCTGATAA GGGAAAGATTTTGACTCAGCTCTCAGTTTTCTGGTTTGATTTTTTG GCACCCTACATAAAGAATCATTTGGTTGCTTCTAATGACAAGGA AGTCTTTGCTTTACTACCATCAAAACTGTCTGAAGAAAAaTACAA ATCTCAATTAGAGGGACGATCCTTGATAGTAAAAAAGCACAGAC TGATACCTTTGGAAGCCATTGTCAGAGGTTACATCACTGGAAGTG CATGGAAAGAGTACAAGAACTCAAAAACTGTCCATGGAGTCAAG GTTGAAAACGAGAACCTTCAAGAGAGCGACGCCTTTCCAACTCC GATTTTCACACCTTCAACGAAAGCTGAACAGGGTGAACACGATG AAAACATCTCTATTGAACAAGCTGCTGAGATTGTAGGTAAAGAC ATTTGTGAGAAGGTCGCTGTCAAGGCGGTCGAGTTGTATTCTGCT GCAAAAAACCTCGCCCTTTTGAAGGGGATCATTATTGCTGATACG AAATTCGAATTTGGACTGGACGAAAACAATGAATTGGTACTAGT AGATGAAGTTTTAACTCCAGATTCTTCTAGATTTTGGAATCAAAA GACTTACCAAGTGGGTAAATCGCAAGAGAGTTACGATAAGCAGT TTCTCAGAGATTGGTTGACGGCCAACGGATTGAATGGCAAAGAG GGCGTAGCCATGGATGCAGAAATTGCTATCAAGAGTAAAGAAAA GTATATTGAAGCTTATGAAGCAATTACTGGCAAGAAATGGGCTT GA 83 Sequence ATGATTAGTACCCTCCTCGCCTTTTTCAGACATCTGAAATTTCCCT of the 3′- TATTCTTCCAATTCCATATAAAATCCTATTTAGGTAATTAGTAAA region that CAATGATCATAAAGTGAAATCATTCAAGTAACCATTCCGTTTATC was used GTTGATTTAAAATCAATAACGAATGAATGTCGGTCTGAGTAGTC to knock AATTTGTTGCCTTGGAGCTCATTGGCAGGGGGTCTTTTGGCTCAG into the TATGGAAGGTTGAAAGGAAAACAGATGGAAAGTGGTTCGTCAGA PpADE1 AAAGAGGTATCCTACATGAAGATGAATGCCAAAGAGATATCTCA locus: AGTGATAGCTGAGTTCAGAATTCTTAGTGAGTTAAGCCATCCCAA CATTGTGAAGTACCTTCATCACGAACATATTTCTGAGAATAAAAC TGTCAATTTATACATGGAATACTGTGATGGTGGAGATCTCTCCAA GCTGATTCGAACACATAGAAGGAACAAAGAGTACATTTCAGAAG AAAAAATATGGAGTATTTTTACGCAGGTTTTATTAGCATTGTATC GTTGTCATTATGGAACTGATTTCACGGCTTCAAAGGAGTTTGAAT CGCTCAATAAAGGTAATAGACGAACCCAGAATCCTTCGTGGGTA GACTCGACAAGAGTTATTATTCACAGGGATATAAAACCCGACAA CATCTTTCTGATGAACAATTCAAACCTTGTCAAACTGGGAGATTT TGGATTAGCAAAAATTCTGGACCAAGAAAACGATTTTGCCAAAA CATACGTCGGTACGCCGTATTACATGTCTCCTGAAGTGCTGTTGG ACCAACCCTACTCACCATTATGTGATATATGGTCTCTTGGGTGCG TCATGTATGAGCTATGTGCATTGAGGCCTCCTT 84 MET16 5′ GGGTGGGCCTGGTAATGTTCACTCCTAGGAACTACTAGAAAAAC TGTGCTAAACGGATTACGTAATTATTATACAAATTCTCTATGGTC TATGGTACATATGGGCTGGTTCAATAATGAATCTATGAAGAATTT GTGCCCATGGGGACCGTTTCTATAAACGTTCTCTTCTTTATGTTTT CCACCTGCTCTTTGAGTTCCGGAAATTCGTTGACAATCTTTTGTCC CAATGTCGATTGGGCGTATTTAAAGCCCAGCTGTTTTCCTCTGAG AAATTGATTCAACTTCCTCACCACCTCCACAAACTCACGCGTGTA TATATCAGGGTTTCTACCGTCTTCGATATAATTGACTACGTCCAC GGGGATGGGAATGTTCAAATCTGTGTTGTGGAGCTTTTGCAAGTG CTCTACAACCTTGTTAATGTTGTTGGAAAGACCCAATTGACTTTC CGCTGTACCGGCGTAATCGTGCACCTGAACACCCAAATGGATGA GGGTTTCGATGAGTTGACTTAGTTCATTTTCAACTTGATCTAATG TTGTCGCAGGTGCACTCATACTTGTCATGGAGAATGAAAGTAAG TTGATAGAGAGCAGACTTCGAGGATGGGATGAACTTGATTAGGT AATCTTTGACAATGTCTTAGAGGTAGGCAGAGGATGCTGGAAAA AAAAAATTGAAAACGCCCAAGCTTCCAGCTTTGCAAGGAAAGAA GAAAAGGGAGTTGCCAGCACGAAATCGGCTTCCTCCGAAAGGTT CACAATTGCAGAATTGTCACCATTCAAATGCCTTTACCCTTCATC TGTGGTACCTCAGGCTAAGAACGGGTCACGTGATATTTCGACACT CATCGCCACAATATGTACTAGCAAGAACTTTTCAGATTTAGTAAT CCGTTCGAAACGGG 85 MET16 3′ CTAGATTTGCACAATATTTGAAAGCTCAGCAAAACATATGAATA TAATTTTTTTTTTCTCTACACTATTTATCCTGTAAGTTTCTGTTTCC CCATGTAGGATCTTTTTCTCCTTCTCTGTCTCCCATTTTTTTTGTTC CCTGTAGTCTTGCCTTGCCTGAGATGCGAGCTCGTCCGCCCATCC AGTCGTGTGAAGGGCCTAGCTTTTCAAAAAGAAAATACCTCCCG CTAAAGGAGGCGTTGCCCCTTCTATCAGTAGTGTCGTAACCAATT TTCACAAACAATAAAAAAAGGACACCAACAACGAAATCAACTAT TTACACACATCCAGATCCGTCCCCCTCCCCATCCAAGAGTTAAAG ACAAATATGGCTGTTAATAATCCGTCTGAATTTAGAAAGAAGTT GGTCGTAGTAGGAGATGGTGCTTGCGGTAAAACTTGTCTATTGAT GGTGTTTGCCGAGGGCGAGTTCCCTCCATCTTATGTTCCAACTGT TTTTGAGAACTATGCCACCCCAGTAGAGGTTGACAACAGAATAG TACAACTCACTCTATGGGATACTGCCGGACAGGAAGATTATGAT AGACTGAGACCTCTTTCCTATCCCGATGCCAATGTGGTCTTGATT TGTTTTGCTATTGACATTCCTGACACCTTAGATAACGTTCAAGAG AAGTGGATTAGTGAGGTGTTGCATTTCTGTCCTGGAGTCCCTATC ATTTTAGTTGGTTGTAAACTTGACTTGAGAAACGATCCAGAGGTT ATCCGTGAATTACAAGCTGTTGGAAAGCAACCAGTCTCCACCAG TGAGGGTCAGGCCGTTGC 86 Sequence CAACTTCCTCACCACCTCCACAAACTCACGCGTGTATATATCAGG of the GTTTCTACCGTCTTCGATATAATTGACTACGTCCACGGGGATGGG PpMET16 AATGTTCAAATCTGTGTTGTGGAGCTTTTGCAAGTGCTCTACAAC auxotrophic CTTGTTAATGTTGTTGGAAAGACCCAATTGACTTTCCGCTGTACC marker: GGCGTAATCGTGCACCTGAACACCCAAATGGATGAGGGTTTCGA TGAGTTGACTTAGTTCATTTTCAACTTGATCTAATGTTGTCGCAG GTGCACTCATACTTGTCATGGAGAATGAAAGTAAGTTGATAGAG AGCAGACTTCGAGGATGGGATGAACTTGATTAGGTAATCTTTGA CAATGTCTTAGAGGTAGGCAGAGGATGCTGGAAAAAAAAAATTG AAAACGCCCAAGCTTCCAGCTTTGCAAGGAAAGAAGAAAAGGG AGTTGCCAGCACGAAATCGGCTTCCTCCGAAAGGTTCACAATTG CAGAATTGTCACCATTCAAATGCCTTTACCCTTCATCTGTGGTAC CTCAGGCTAAGAACGGGTCACGTGATATTTCGACACTCATCGCC ACAATATGTACTAGCAAGAACTTTTCAGATTTAGTAATCCGTTCG AAACGGGAAAAAATGTTTTTACCCTTCTATCAACTGCTAATCTTT CTAGGTTTATACTGCCAGCAGCCCGTTCCAGATACCAACATGCCA TTCACTATAGGCCAGTCAAAAACCAGTTTGAACCTCTCCAAGGTC CAAGTGGACCACCTTAACCTTTCTCTTCAGAATCTCAGTCCAGAA GAAATCATACAATGGTCTATCATTACCTTCCCACACCTGTATCAA ACTACGGCATTCGGATTGACTGGGTTGTGTATAACTGACATGGTT CACAAAATAACAGCCAAAAGAGGCAAAAAGCATGCTATTGACTT GATTTTCATAGACACCTTACATCATTTTCCACAGACTTTAGATCT CGTTGAACGAGTCAAAGATAAATACCACTGCAATGTTCATGTCTT CAAACCACAGAATGCCACTACTGAGCTCGAGTTTGGGGCGCAAT ATGGCGAAAACTTATGGGAAACAGATGATAACAAGTATGACTAC CTCGTAAAAGTTGAACCCTCACAACGTGCCTACCATGCATTAGAC GTCTGCGCCGTCTTCACAGGAAGAAGACGGTCTCAAGGTGGTAA AAGGGGAGAATTGCCCGTGATTGAAATTGATGAAATTTCTCAGG TGGTCAAGATTAATCCGTTAGCATCCTGGGGGTTTGAACAAGTTC AAAACTATATCCAAGCTAATAGCGTTCCATACAACGAATTGCTG GATTTGGGATACAAGTCAGTTGGAGATTACCATTCCACACAACC CACTAAAAATGGTGAAGATGAAAGAGCAGGCAGGTGGAGAGGT AAACAAAAGAGTGAGTGTGGTATCCACGAAGCTTCTAGATTTGC ACAATATTTGAAAGCTCAGCAAAACATATGAATATAATTTTTTTT TTCTCTACACTATTTATCCTGTAAGTTTCTGTTTCCCCATGTAGGA TCTTTTTCTCCTTCTCTGTCTCCCATTTTTTTTGTTCCCTGTAGTCT TGCCTTGCCTGAGATGCGAGCTCGTCCGCCCATCCAGTCGTGTGA AGGGCCTAGCTTTTCAAAAAGAAAATACCTCCCGCTAAAGGAGG CGTTGCCCCTTCTATCAGTAGTGTCGTAACCAATTTTCACAAACA ATAAAAAAAGGACACCAACAACGAAATCAACTATTTACACACAT CCAGATCCGTCCC 87 Sequence TAACTGGCCCTTTGACGTTTCTGACAATAGTTCTAGAGGAGTCGT of the 5′- CCAAAAACTCAACTCTGACTTGGGTGACACCACCACGGGATCCG Region GTTCTTCCGAGGACCTTGATGACCTTGGCTAATGTAACTGGAGTT used for TTAGTATCCATTTTAAGATGTGTGTTTCTGTAGGTTCTGGGTTGG knock out AAAAAAATTTTAGACACCAGAAGAGAGGAGTGAACTGGTTTGCG of PpHIS1: TGGGTTTAGACTGTGTAAGGCACTACTCTGTCGAAGTTTTAGATA GGGGTTACCCGCTCCGATGCATGGGAAGCGATTAGCCCGGCTGT TGCCCGTTTGGTTTTTGAAGGGTAATTTTCAATATCTCTGTTTGAG TCATCAATTTCATATTCAAAGATTCAAAAACAAAATCTGGTCCAA GGAGCGCATTTAGGATTATGGAGTTGGCGAATCACTTGAACGAT AGACTATTATTTGC 88 Sequence GTGACATTCTTGTCTTTGAGATCAGTAATTGTAGAGCATAGATAG of the 3′- AATAATATTCAAGACCAACGGCTTCTCTTCGGAAGCTCCAAGTA Region GCTTATAGTGATGAGTACCGGCATATATTTATAGGCTTAAAATTT used for CGAGGGTTCACTATATTCGTTTAGTGGGAAGAGTTCCTTTCACTC knock out TTGTTATCTATATTGTCAGCGTGGACTGTTTATAACTGTACCAAC of PpHIS1: TTAGTTTCTTTCAACTCCAGGTTAAGAGACATAAATGTCCTTTGA TGCTGACAATAATCAGTGGAATTCAAGGAAGGACAATCCCGACC TCAATCTGTTCATTAATGAAGAGTTCGAATCGTCCTTAAATCAAG CGCTAGACTCAATTGTCAATGAGAACCCTTTCTTTGACCAAGAAA CTATAAATAGATCGAATGACAAAGTTGGAAATGAGTCCATTAGC TTACATGATATTGAGCAGGCAGACCAAAATAAACCGTCCTTTGA GAGCGATATTGATGGTTCGGCGCCGTTGATAAGAGACGACAAAT TGCCAAAGAAACAAAGCTGGGGGCTGAGCAATTTTTTTTCAAGA AGAAATAGCATATGTTTACCACTACATGAAAATGATTCAAGTGTT GTTAAGACCGAAAGATCTATTGCAGTGGGAACACCCCATCTTCA ATACTGCTTCAATGGAATCTCCAATGCCAAGTACAATGCATTTAC CTTTTTCCCAGTCATCCTATACGAGCAATTCAAATTTTTTTTCAAT TTATACTTTACTTTAGTGGCTCTCTCTCAAGCGATACCGCAACTTC GCATTGGATATCTTTCTTCGTATGTCGTCCCACTTTTGTTTGTACT CATAGTGACCATGTCAAAAGAGGCGATGGATGATATTCAACGCC GAAGAAGGGATAGAGAACAGAACAATGAACCATATGAGGTTCT GTCCAGCCCATCACCAGTTTTGTCCAAAAACTTAAAATGTGGTCA CTTGGTTCGATTGCATAAGGGAATGAGAGTGCCCGCAGATATGG TTCTTGTCCAGTCAAGCGAATCCACCGGAGAGTCATTTATCAAGA CAGATCAGCTGGATGGTGAGACTGATTGGAAGCTTCGGATTGTTT CTCCAGTTACACAATCGTTACCAATGACTGAACTTCAAAATGTCG CCATCACTGCAAGCGCACCCTCAAAATCAATTCACTCCTTTCTTG GAAGATTGACCTACAATGGGCAATCATATGGTCTTACGATAGAC AACACAATGTGGTGTAATACTGTATTAGCTTCTGGTTCAGCAATT GGTTGTATAATTTACACAGGTAAAGATACTCGACAATCGATGAA CACAACTCAGCCCAAACTGAAAACGGGCTTGTTAGAACTGGAAA TCAATAGTTTGTCCAAGATCTTATGTGTTTGTGTGTTTGCATTATC TGTCATCTTAGTGCTATTCCAAGGAATAGCTGATGATTGGTACGT CGATATCATGCGGTTTCTCATTCTATTCTCCACTATTATCCCAGTG TCTCTGAGAGTTAACCTTGATCTTGGAAAGTCAGTCCATGCTCAT CAAATAGAAACTGATAGCTCAATACCTGAAACCGTTGTTAGAAC TAGTACAATACCGGAAGACCTGGGAAGAATTGAATACCTATTAA GTGACAAAACTGGAACTCTTACTCAAAATGATATGGAAATGAAA AAACTACACCTAGGAACAGTCTCTTATGCTGGTGATACCATGGAT ATTATTTCTGATCATGTTAAAGGTCTTAATAACGCTAAAACATCG AGGAAAGATCTTGGTATGAGAATAAGAGATTTGGTTACAACTCT GGCCATCTG 89 Sequence CAAGTTGCGTCCGGTATACGTAACGTCTCACGATGATCAAAGAT of the AATACTTAATCTTCATGGTCTACTGAATAACTCATTTAAACAATT PpHIS1 GACTAATTGTACATTATATTGAACTTATGCATCCTATTAACGTAA auxotrophic TCTTCTGGCTTCTCTCTCAGACTCCATCAGACACAGAATATCGTT marker: CTCTCTAACTGGTCCTTTGACGTTTCTGACAATAGTTCTAGAGGA GTCGTCCAAAAACTCAACTCTGACTTGGGTGACACCACCACGGG ATCCGGTTCTTCCGAGGACCTTGATGACCTTGGCTAATGTAACTG GAGTTTTAGTATCCATTTTAAGATGTGTGTTTCTGTAGGTTCTGG GTTGGAAAAAAATTTTAGACACCAGAAGAGAGGAGTGAACTGGT TTGCGTGGGTTTAGACTGTGTAAGGCACTACTCTGTCGAAGTTTT AGATAGGGGTTACCCGCTCCGATGCATGGGAAGCGATTAGCCCG GCTGTTGCCCGTTTGGTTTTTGAAGGGTAATTTTCAATATCTCTGT TTGAGTCATCAATTTCATATTCAAAGATTCAAAAACAAAATCTGG TCCAAGGAGCGCATTTAGGATTATGGAGTTGGCGAATCACTTGA ACGATAGACTATTATTTGCTGTTCCTAAAGAGGGCAGATTGTATG AGAAATGCGTTGAATTACTTAGGGGATCAGATATTCAGTTTCGA AGATCCAGTAGATTGGATATAGCTTTGTGCACTAACCTGCCCCTG GCATTGGTTTTCCTTCCAGCTGCTGACATTCCCACGTTTGTAGGA GAGGGTAAATGTGATTTGGGTATAACTGGTATTGACCAGGTTCA GGAAAGTGACGTAGATGTCATACCTTTATTAGACTTGAATTTCGG TAAGTGCAAGTTGCAGATTCAAGTTCCCGAGAATGGTGACTTGA AAGAACCTAAACAGCTAATTGGTAAAGAAATTGTTTCCTCCTTTA CTAGCTTAACCACCAGGTACTTTGAACAACTGGAAGGAGTTAAG CCTGGTGAGCCACTAAAGACAAAAATCAAATATGTTGGAGGGTC TGTTGAGGCCTCTTGTGCCCTAGGAGTTGCCGATGCTATTGTGGA TCTTGTTGAGAGTGGAGAAACCATGAAAGCGGCAGGGCTGATCG ATATTGAAACTGTTCTTTCTACTTCCGCTTACCTGATCTCTTCGAA GCATCCTCAACACCCAGAACTGATGGATACTATCAAGGAGAGAA TTGAAGGTGTACTGACTGCTCAGAAGTATGTCTTGTGTAATTACA ACGCACCTAGAGGTAACCTTCCTCAGCTGCTAAAACTGACTCCA GGCAAGAGAGCTGCTACCGTTTCTCCATTAGATGAAGAAGATTG GGTGGGAGTGTCCTCGATGGTAGAGAAGAAAGATGTTGGAAGAA TCATGGACGAATTAAAGAAACAAGGTGCCAGTGACATTCTTGTC TTTGAGATCAGTAATTGTAGAGCATAGATAGAATAATATTCAAG ACCAACGGCTTCTCTTCGGAAGCTCCAAGTAGCTTATAGTGATGA GTACCGGCATATATTTATAGGCTTAAAATTTCGAGGGTTCACTAT ATTCGTTTAGTGGGAAGAGTTCCTTTCACTCTTGTTATCTATATTG TCAGCGTGGACTGTTTATAACTGTACCAACTTAGTTTCTTTCAAC TCCAGGTTAAGAGACATAAATGTCCTTTGATGC 90 Sequence GAAGGGCCATCGAATTGTCATCGTCTCCTCAGGTGCCATCGCTGT of the 5′- GGGCATGAAGAGAGTCAACATGAAGCGGAAACCAAAAAAGTTA region that CAGCAAGTGCAGGCATTGGCTGCTATAGGACAAGGCCGTTTGAT was used AGGACTTTGGGACGACCTTTTCCGTCAGTTGAATCAGCCTATTGC to knock GCAGATTTTACTGACTAGAACGGATTTGGTCGATTACACCCAGTT into the TAAGAACGCTGAAAATACATTGGAACAGCTTATTAAAATGGGTA PpPRO1 TTATTCCTATTGTCAATGAGAATGACACCCTATCCATTCAAGAAA locus: TCAAATTTGGTGACAATGACACCTTATCCGCCATAACAGCTGGTA TGTGTCATGCAGACTACCTGTTTTTGGTGACTGATGTGGACTGTC TTTACACGGATAACCCTCGTACGAATCCGGACGCTGAGCCAATC GTGTTAGTTAGAAATATGAGGAATCTAAACGTCAATACCGAAAG TGGAGGTTCCGCCGTAGGAACAGGAGGAATGACAACTAAATTGA TCGCAGCTGATTTGGGTGTATCTGCAGGTGTTACAACGATTATTT GCAAAAGTGAACATCCCGAGCAGATTTTGGACATTGTAGAGTAC AGTATCCGTGCTGATAGAGTCGAAAATGAGGCTAAATATCTGGT CATCAACGAAGAGGAAACTGTGGAACAATTTCAAGAGATCAATC GGTCAGAACTGAGGGAGTTGAACAAGCTGGACATTCCTTTGCAT ACACGTTTCGTTGGCCACAGTTTTAATGCTGTTAATAACAAAGAG TTTTGGTTACTCCATGGACTAAAGGCCAACGGAGCCATTATCATT GATCCAGGTTGTTATAAGGCTATCACTAGAAAAAACAAAGCTGG TATTCTTCCAGCTGGAATTATTTCCGTAGAGGGTAATTTCCATGA ATACGAGTGTGTTGATGTTAAGGTAGGACTAAGAGATCCAGATG ACCCACATTCACTAGACCCCAATGAAGAACTTTACGTCGTTGGCC GTGCCCGTTGTAATTACCCCAGCAATCAAATCAACAAAATTAAG GGTCTACAAAGCTCGCAGATCGAGCAGGTTCTAGGTTACGCTGA CGGTGAGTATGTTGTTCACAGGGACAACTTGGCTTTCCCAGTATT TGCCGATCCAGAACTGTTGGATGTTGTTGAGAGTACCCTGTCTGA ACAGGAGAGAGAATCCAAACCAAATAAATAG 91 Sequence AATTTCACATATGCTGCTTGATTATGTAATTATACCTTGCGTTCG of the 3′- ATGGCATCGATTTCCTCTTCTGTCAATCGCGCATCGCATTAAAAG region that TATACTTTTTTTTTTTTCCTATAGTACTATTCGCCTTATTATAAACT was used TTGCTAGTATGAGTTCTACCCCCAAGAAAGAGCCTGATTTGACTC to knock CTAAGAAGAGTCAGCCTCCAAAGAATAGTCTCGGTGGGGGTAAA into the GGCTTTAGTGAGGAGGGTTTCTCCCAAGGGGACTTCAGCGCTAA PpPRO1 GCATATACTAAATCGTCGCCCTAACACCGAAGGCTCTTCTGTGGC locus: TTCGAACGTCATCAGTTCGTCATCATTGCAAAGGTTACCATCCTC TGGATCTGGAAGCGTTGCTGTGGGAAGTGTGTTGGGATCTTCGCC ATTAACTCTTTCTGGAGGGTTCCACGGGCTTGATCCAACCAAGAA TAAAATAGACGTTCCAAAGTCGAAACAGTCAAGGAGACAAAGTG TTCTTTCTGACATGATTTCCACTTCTCATGCAGCTAGAAATGATC ACTCAGAGCAGCAGTTACAAACTGGACAACAATCAGAACAAAA AGAAGAAGATGGTAGTCGATCTTCTTTTTCTGTTTCTTCCCCCGC AAGAGATATCCGGCACCCAGATGTACTGAAAACTGTCGAGAAAC ATCTTGCCAATGACAGCGAGATCGACTCATCTTTACAACTTCAAG GTGGAGATGTCACTAGAGGCATTTATCAATGGGTAACTGGAGAA AGTAGTCAAAAAGATAACCCGCCTTTGAAACGAGCAAATAGTTT TAATGATTTTTCTTCTGTGCATGGTGACGAGGTAGGCAAGGCAGA TGCTGACCACGATCGTGAAAGCGTATTCGACGAGGATGATATCT CCATTGATGATATCAAAGTTCCGGGAGGGATGCGTCGAAGTTTTT TATTACAAAAGCATAGAGACCAACAACTTTCTGGACTGAATAAA ACGGCTCACCAACCAAAACAACTTACTAAACCTAATTTCTTCACG AACAACTTTATAGAGTTTTTGGCATTGTATGGGCATTTTGCAGGT GAAGATTTGGAGGAAGACGAAGATGAAGATTTAGACAGTGGTTC CGAATCAGTCGCAGTCAGTGATAGTGAGGGAGAATTCAGTGAGG CTGACAACAATTTGTTGTATGATGAAGAGTCTCTCCTATTAGCAC CTAGTACCTCCAACTATGCGAGATCAAGAATAGGAAGTATTCGT ACTCCTACTTATGGATCTTTCAGTTCAAATGTTGGTTCTTCGTCTA TTCATCAGCAGTTAATGAAAAGTCAAATCCCGAAGCTGAAGAAA CGTGGACAGCACAAGCATAAAACACAATCAAAAATACGCTCGAA GAAGCAAACTACCACCGTAAAAGCAGTGTTGCTGCTATTAAA 92 Truncated GCTCCACCAAGATTGATTTGTGACTCCAGAGTTTTGGAGAGATAC hEPO TTGTTGGAGGCTAAAGAGGCTGAGAACATCACTACTGGTTGTGC DNA TGAACACTGTTCCTTGAACGAGAACATCACAGTTCCAGACACTA (codon AGGTTAACTTCTACGCTTGGAAGAGAATGGAAGTTGGACAACAG optimized) GCTGTTGAAGTTTGGCAAGGATTGGCTTTGTTGTCCGAGGCTGTT TTGAGAGGTCAAGCTTTGTTGGTTAACTCCTCCCAACCATGGGAA CCATTGCAATTGCACGTTGACAAGGCTGTTTCTGGATTGAGATCC TTGACTACTTTGTTGAGAGCTTTGGGTGCTCAGAAAGAGGCTATT TCTCCACCAGATGCTGCTTCAGCTGCTCCATTGAGAACTATCACT GCTGACACTTTCAGAAAGTTGTTCAGAGTTTACTCCAACTTCTTG AGAGGAAAGTTGAAGTTGTACACTGGTGAAGCTTGTAGAACTGG TGACTAGTAA 93 Truncated APPRLICDSR VLERYLLEAK EAENITTGCA EHCSLNENIT VPDTKVNFYA hEPO WKRMEVGQQA VEVWQGLALL SEAVLRGQAL LVNSSQPWEP protein LQLHVDKAVS GLRSLTTLLR ALGAQKEAIS PPDAASAAPL RTITADTFRK LFRVYSNFLR GKLKLYTGEA CRTGD 94 Chicken ATGCTGGGTAAGAACGACCCAATGTGTCTTGTTTTGGTCTTGTTG lysosome GGATTGACTGCTTTGTTGGGTATCTGTCAAGGT signal DNA (CLSP) 95 Chicken MLGKNDPMCLVLVLLGLTALLGICQG lysosome signal peptide (CLSP) 96 Sequence ATGGATTCTCAGGTAATAGGTATTCTAGGAGGAGGCCAGCTAGG of the CCGAATGATTGTTGAGGCCGCTAGCAGGCTCAATATCAAGACCG PpAde2 TGATTCTTGATGATGGTTTTTCACCTGCTAAGCACATTAATGCTG gene CGCAAGACCACATCGACGGATCATTCAAAGATGAGGAGGCTATC without its GCCAAGTTAGCTGCCAAATGTGATGTTCTCACTGTAGAGATTGAG promoter CATGTCAACACAGATGCTCTAAAGAGAGTTCAAGACAGAACTGG but AATCAAGATATATCCTTTACCAGAGACAATCGAACTAATCAAGG including ATAAGTACTTGCAAAAGGAACATTTGATCAAGCACAACATTTCG its GTGACAAAGTCTCAGGGTATAGAATCTAATGAAAAGGCGCTGCT termination TTTGTTTGGAGAAGAGAATGGATTTCCATATCTGTTGAAGTCCCG sequences GACTATGGCTTATGATGGAAGAGGCAATTTTGTAGTGGAGTCTA AAGAGGACATCAGTAAGGCATTAGAATTCTTGAAAGATCGTCCA TTGTATGCCGAGAAGTTTGCTCCTTTTGTTAAAGAATTAGCGGTA ATGGTTGTGAGATCACTGGAAGGCGAAGTATTCTCCTACCCAAC CGTAGAAACTGTGCACAAGGACAATATCTGTCATATTGTGTATGC TCCGGCCAGAGTTAATGACACCATCCAAAAGAAAGCTCAAATAT TAGCTGAAAACACTGTGAAGACTTTCCCAGGCGCTGGAATCTTC GGAGTTGAGATGTTCCTATTGTCTGATGGAGAACTTCTTGTAAAT GAGATTGCTCCAAGGCCCCACAATTCTGGTCACTATACAATCGAT GCATGTGTAACATCTCAGTTCGAAGCACATGTAAGAGCCATAAC TGGTCTGCCAATGCCACTAGATTTCACCAAACTATCTACTTCCAA CACCAACGCTATTATGCTCAATGTTTTGGGTGCTGAAAAATCTCA CGGGGAATTAGAGTTTTGTAGAAGAGCCTTAGAAACACCCGGTG CTTCTGTATATCTGTACGGAAAGACCACCCGATTGGCTCGTAAGA TGGGTCATATCAACATAATAGGATCTTCCATGTTGGAAGCAGAA CAAAAGTTAGAGTACATTCTAGAAGAATCAACCCACTTACCATC CAGTACTGTATCAGCTGACACTAAACCGTTGGTTGGAGTTATCAT GGGTTCAGACTCTGATCTACCTGTGATTTCGAAAGGTTGCGATAT TTTAAAACAGTTTGGTGTTCCATTCGAAGTTACTATTGTCTCTGCT CATAGAACACCACAGAGAATGACCAGATATGCCTTTGAAGCCGC TAGTAGAGGTATCAAGGCTATCATTGCAGGTGCTGGTGGTGCTG CTCATCTTCCAGGAATGGTTGCTGCCATGACTCCGTTGCCAGTCA TTGGTGTTCCTGTCAAGGGCTCTACGTTGGATGGTGTAGACTCGC TACACTCGATTGTCCAAATGCCTAGAGGTGTTCCTGTGGCTACGG TTGCTATCAACAACGCCACCAATGCCGCTCTGTTGGCCATCAGGA TTTTAGGTACAATTGACCACAAATGGCAAAAGGAAATGTCCAAG TATATGAATGCAATGGAGACCGAAGTGTTGGGGAAGGCATCCAA CTTGGAATCTGAAGGGTATGAATCCTATTTGAAGAATCGTCTTTG AATTTAGTATTGTTTTTTAATAGATGTATATATAATAGTACACGTAACTT ATCTATTCCATTCATAATTTTATTTTAAAGGTTCGGTAGAAATTTGTCCT CCAAAAAGTTGGTTAGAGCCTGGCAGTTTTGATAGGCATTATTATAGA TTGGGTAATATTTACCCTGCACCTGGAGGAACTTTGCAAAGAGCCTCA TGTGC 97 PpADE2 MDSQVIGILGGGQLGRMIVEAASRLNIKTVILDDGFSPAKHINAAQD HIDGSFKDEEAIAKLAAKCDVLTVEIEHVNTDALKRVQDRTGIKIYP LPETIELIKDKYLQKEHLIKHNISVTKSQGIESNEKALLLFGEENGFPY LLKSRTMAYDGRGNFVVESKEDISKALEFLKDRPLYAEKFAPFVKE LAVMVVRSLEGEVFSYPTVETVHKDNICHIVYAPARVNDTIQKKAQ ILAENTVKTFPGAGIFGVEMFLLSDGELLVNEIAPRPHNSGHYTIDAC VTSQFEAHVRAITGLPMPLDFTKLSTSNTNAIMLNVLGAEKSHGELE FCRRALETPGASVYLYGKTTRLARKMGHINIIGSSMLEAEQKLEYIL EESTHLPSSTVSADTKPLVGVIMGSDSDLPVISKGCDILKQFGVPFEV TIVSAHRTPQRMTRYAFEAASRGIKAIIAGAGGAAHLPGMVAAMTP LPVIGVPVKGSTLDGVDSLHSIVQMPRGVPVATVAINNATNAALLAI RILGTIDHKWQKEMSKYMNAMETEVLGKASNLESEGYESYLKNRL 98 Pp TRP2: ACTGGGCCTTTAGAGGGTGCTGAAGTTGACCCCTTGGTGCTTCTG 5′ and ORF GAAAAAGAACTGAAGGGCACCAGACAAGCGCAACTTCCTGGTAT TCCTCGTCTAAGTGGTGGTGCCATAGGATACATCTCGTACGATTG TATTAAGTACTTTGAACCAAAAACTGAAAGAAAACTGAAAGATG TTTTGCAACTTCCGGAAGCAGCTTTGATGTTGTTCGACACGATCG TGGCTTTTGACAATGTTTATCAAAGATTCCAGGTAATTGGAAACG TTTCTCTATCCGTTGATGACTCGGACGAAGCTATTCTTGAGAAAT ATTATAAGACAAGAGAAGAAGTGGAAAAGATCAGTAAAGTGGT ATTTGACAATAAAACTGTTCCCTACTATGAACAGAAAGATATTAT TCAAGGCCAAACGTTCACCTCTAATATTGGTCAGGAAGGGTATG AAAACCATGTTCGCAAGCTGAAAGAACATATTCTGAAAGGAGAC ATCTTCCAAGCTGTTCCCTCTCAAAGGGTAGCCAGGCCGACCTCA TTGCACCCTTTCAACATCTATCGTCATTTGAGAACTGTCAATCCTT CTCCATACATGTTCTATATTGACTATCTAGACTTCCAAGTTGTTG GTGCTTCACCTGAATTACTAGTTAAATCCGACAACAACAACAAA ATCATCACACATCCTATTGCTGGAACTCTTCCCAGAGGTAAAACT ATCGAAGAGGACGACAATTATGCTAAGCAATTGAAGTCGTCTTT GAAAGACAGGGCCGAGCACGTCATGCTGGTAGATTTGGCCAGAA ATGATATTAACCGTGTGTGTGAGCCCACCAGTACCACGGTTGATC GTTTATTGACTGTGGAGAGATTTTCTCATGTGATGCATCTTGTGT CAGAAGTCAGTGGAACATTGAGACCAAACAAGACTCGCTTCGAT GCTTTCAGATCCATTTTCCCAGCAGGTACCGTCTCCGGTGCTCCG AAGGTAAGAGCAATGCAACTCATAGGAGAATTGGAAGGAGAAA AGAGAGGTGTTTATGCGGGGGCCGTAGGACACTGGTCGTACGAT GGAAAATCGATGGACACATGTATTGCCTTAAGAACAATGGTCGT CAAGGACGGTGTCGCTTACCTTCAAGCCGGAGGTGGAATTGTCT ACGATTCTGACCCCTATGACGAGTACATCGAAACCATGAACAAA ATGAGATCCAACAATAACACCATCTTGGAGGCTGAGAAAATCTG GACCGATAGGTTGGCCAGAGACGAG AATCAAAGTGAATCCGAAGAAAACGATCAATGA 99 PpTRP2 3′ ACGGAGGACGTAAGTAGGAATTTATGTAATCATGCCAATACATC region TTTAGATTTCTTCCTCTTCTTTTTAACGAAAGACCTCCAGTTTTGC ACTCTCGACTCTCTAGTATCTTCCCATTTCTGTTGCTGCAACCTCT TGCCTTCTGTTTCCTTCAATTGTTCTTCTTTCTTCTGTTGCACTTGG CCTTCTTCCTCCATCTTTCGTTTTTTTTCAAGCCTTTTCAGCAGTTC TTCTTCCAAGAGCAGTTCTTTGATTTTCTCTCTCCAATCCACCAAA AAACTGGATGAATTCAACCGGGCATCATCAATGTTCCACTTTCTT TCTCTTATCAATAATCTACGTGCTTCGGCATACGAGGAATCCAGT TGCTCCCTAATCGAGTCATCCACAAGGTTAGCATGGGCCTTTTTC AGGGTGTCAAAAGCATCTGGAGCTCGTTTATTCGGAGTCTTGTCT GGATGGATCAGCAAAGACTTTTTGCGGAAAGTCTTTCTTATATCT TCCGGAGAACAACCTGGTTTCAAATCCAAGATGGCATAGCTGTC CAATTTGAAAGTGGAAAGAATCCTGCCAATTTCCTTCTCTCGTGT CAGCTCGTTCTCCTCCTTTTGCAACAGGTCCACTTCATCTGGCATT TTTCTTTATGTTAACTTTAATTATTATTAATTATAAAGTTGATTAT CGTTATCAAAATAATCATATTCGAGAAATAATCCGTCCATGCAAT ATATAAATAAGAATTCATAATAATGTAATGATAACAGTACCTCT GATGACCTTTGATGAACCGCAATTTTCTTTCCAATGACAAGACAT CCCTATAATACAATTATACAGTTTATATATCACAAATAATCACCT TTTTATAAGAAAACCGTCCTCTCCGTAACAGAACTTATTATCCGC ACGTTATGGTTAACACACTACTAATACCGATATAGTGTATGAAGT CGCTACGAGATAGCCATCCAGGAAACTTACCAATTCATCAGCAC TTTCATGATCCGATTGTTGGCTTTATTCTTTGCGAGACAGATACTT GCCAATGAAATAACTGATCCCACAGATGAGAATCCGGTGCTCGT 100 Pp ADE2 CTTAAAATCATCTGCCTCACCCCACCGACCAATGGGAATTCTAGA 5′ region AACAATTTCATTGCTCTTCTTCTCGTTACCATAAGAATCGGCTGT CATGTTTGACTTAACGAACCCTGGAACAAGGGAATTCACGGTAA TACCTTTTGGAGCAAGTTCAACCGATAGAGCCTTCATTAATGAGT TGATTGCACCTTTGGTGGTCGCATATACCGATTGATTCGGGTAGG TCACTTCGAAACTGTACAGGGAGGCAGTAAAGATGATCCTACCC TTAATCTGGTTCTTAATAAAGTGTTTAGTGACTAGCTGTGTCAAT CTAAATGGAAAATCGACATTTACCTTTTGGATAGCCGCGTAATCT TTCTCCGTAAAACTTGTAAACTCAGATTTAATGGCAATGGCAGCG TTGTTGATTAAAATGTCAATCTTTCCAGTGGAACTCTTCTCCACC GCAGGACTCGTTACGGTCTCTTCCAGCTTTGCAAGATCGGCATCC ACTAGATCCAACTCAATTGTATGTATGGAGGCACCATCGGCATTT GACATTCTCACCTCTTCAATGAAAGCCGTTGGGTCTGTAGAAGGT CTATGGATAAGAATAAGTTCTGCACCTGCTTCATAAAGTCCTCGA ACTATTCCTTGGCCTAATCCGCTGGTACCACCGGTGATCAAGGCG ACCTTACCATTCAAAGAAAACAAATCAGCGGACATTAGCGACTT GAATAGGGAATGGGTTAGACAAATGAAAGCCGACGAGCCAGCA CTTTATAGTAAGTGCAGGTGAGTCAATAAGAATAAATGTATGGC TTGCTGTCCCTATCGCGTAAGAAGCTTACTAAGATCGCCTAAATT GAAAAGTTGAACAAATCAGTTCTAGCTGGCCTCCATCAGCATTTC GTTCTCCTCTGATCATCTTTGCCAATCGCTAGCATGCCCTCAGCG TGCAAGGAAAAGCACGCTTCTTTCTTATCGACGTATTTTCAACTA TGGCAGAGCCAGGTTAGCAAGTC 101 Pp ADE2 ATTTAGTATTGTTTTTTAATAGATGTATATATAATAGTACACGTA 3′ region ACTTATCTATTCCATTCATAATTTTATTTTAAAGGTTCGGTAGAA ATTTGTCCTCCAAAAAGTTGGTTAGAGCCTGGCAGTTTTGATAGG CATTATTATAGATTGGGTAATATTTACCCTGCACCTGGAGGAACT TTGCAAAGAGCCTCATGTGCTCTAAAAGGATGTCAGAATTCCAA CATTTCAAAATTATATCTGCATGCGTCTGTAATACTGGAACTGTT ATTTTTCTGGTCAGGATTTCACCGCTCTTGTCGTCATGTTTCTCGT CGTCTGAAAGTAAACTGACTTTCCTCTTTCCATAAACACAAAAAT CGATTGCAACTTGGTTATTCTTGAGATTGAAATTTGCTGTGTCTTC AGTGCTTAGCTGAATATCAACAAACTTACTTAGTACTAATAACGA AGCACTATGGTAAGTGGCATAACATAGTGGTATTGAAGCGAACA GTGGATATTGAACCCAAGCATTGGCAACATCTGGCTCTGTTGATA CTGATCCGGATCGTTTGGCACCAATTCCTGAAACGGCGTAGTGCC ACCAAGGTTTCGATTTGAGAACAGGTTCATCATCAGAGTCAACC ACCCCAATGTCAATGGCAGGCTCCAACGAAGTAGGTCCAACAAC AACAGGAAGTATTTGACCTTGAAGATCTGTTCCTTTATGATCCAC CACACCTTGCCCCAATTCCAATAACTTTACCAGTCCCGATGCAGA CATGATAACTGGTACTAATGATCTCCATTGATTTTCGTCGGCACT ACGTAAAGCCTCCAAAAATGAATTCAGAATATCTTCTGAAACTA GATTCTGCTTCTGTGATTCAAGCATTGCTTTATGTAGACATCTCTT GAATAAAAGCAATTCTCCACATATTGGTGTGTGTAAGATAGATCT GGAAAGATGTATCTGGAATAGTCCAGTCAACGTTGTGCAATTGA TTAGCATTACCTTACTGTGAACATCTCTATCTACAACAACAGACT CAATTCGATAGACGTTCCGGGAAAGTTTTTCAAGCGCATTCAGTT TGCTGTTGAACAAAGTGACTTTGCTTTCCAATGTGCAAATACCCC TGTATATCAAGTCCATCACATCACTCAAGACCTTGGTGGAAAAG AATGAAACAGCTGGAGCATAATTTTCGAATGAATTAGGTAAGGT CACTTCATCCTTATCTGTTGTAATGCTATAATCAATAGCGGAACT AACATCTTCCCATGTAACAGGTTTCTTGATCTCTGAATCTGAATC TTTATTTGAAAAAGAATTGAAAAAAGACTCATCACTCATTGGGA ATTCAAGGTCATTAGGGTATTCCATTGTTAGTTCTGGTCTAGGTT TAAAGGGATCACCTTCGTTAAGACGATGGAAAATAGCTAATCTG TACAATAACCAGATACTTCTAACGAAGCTCTCTCTATCCATCAGT TGACGTGTTGAGGATATCTGAACTAGCTCTTTCCACTGCGAATCA GGCATGCTCGTATAGCTGGCAAGCATGTTATTCAGCTTTACCAAG TTAGAAGCCCTTTGGAAACCATCTATAGATTCCCGAAAAAACTTA TACCCACTGAGGGTTTCACTGAGCATAGTCAGTGACATCAAAGA GCATTTCAAATCCATCTCA 102 NATR ATGGGTACCACTCTTGACGACACGGCTTACCGGTACCGCACCAG ORF TGTCCCGGGGGACGCCGAGGCCATCGAGGCACTGGATGGGTCCT TCACCACCGACACCGTCTTCCGCGTCACCGCCACCGGGGACGGC TTCACCCTGCGGGAGGTGCCGGTGGACCCGCCCCTGACCAAGGT GTTCCCCGACGACGAATCGGACGACGAATCGGACGACGGGGAG GACGGCGACCCGGACTCCCGGACGTTCGTCGCGTACGGGGACGA CGGCGACCTGGCGGGCTTCGTGGTCGTCTCGTACTCCGGCTGGAA CCGCCGGCTGACCGTCGAGGACATCGAGGTCGCCCCGGAGCACC GGGGGCACGGGGTCGGGCGCGCGTTGATGGGGCTCGCGACGGA GTTCGCCCGCGAGCGGGGCGCCGGGCACCTCTGGCTGGAGGTCA CCAACGTCAACGCACCGGCGATCCACGCGTACCGGCGGATGGGG TTCACCCTCTGCGGCCTGGACACCGCCCTGTACGACGGCACCGCC TCGGACGGCGAGCAGGCGCTCTACATGAGCATGCCCTGCCCCTA ATCAGTACTG 103 HygR ORF ATGGGTAAAAAGCCTGAACTCACCGCGACGTCTGTCGAGAAGTT TCTGATCGAAAAGTTCGACAGCGTCTCCGACCTGATGCAGCTCTC GGAGGGCGAAGAATCTCGTGCTTTCAGCTTCGATGTAGGAGGGC GTGGATATGTCCTGCGGGTAAATAGCTGCGCCGATGGTTTCTACA AAGATCGTTATGTTTATCGGCACTTTGCATCGGCCGCGCTCCCGA TTCCGGAAGTGCTTGACATTGGGGAATTCAGCGAGAGCCTGACC TATTGCATCTCCCGCCGTGCACAGGGTGTCACGTTGCAAGACCTG CCTGAAACCGAACTGCCCGCTGTTCTGCAGCCGGTCGCGGAGGC CATGGATGCGATCGCTGCGGCCGATCTTAGCCAGACGAGCGGGT TCGGCCCATTCGGACCGCAAGGAATCGGTCAATACACTACATGG CGTGATTTCATATGCGCGATTGCTGATCCCCATGTGTATCACTGG CAAACTGTGATGGACGACACCGTCAGTGCGTCCGTCGCGCAGGC TCTCGATGAGCTGATGCTTTGGGCCGAGGACTGCCCCGAAGTCC GGCACCTCGTGCACGCGGATTTCGGCTCCAACAATGTCCTGACG GACAATGGCCGCATAACAGCGGTCATTGACTGGAGCGAGGCGAT GTTCGGGGATTCCCAATACGAGGTCGCCAACATCTTCTTCTGGAG GCCGTGGTTGGCTTGTATGGAGCAGCAGACGCGCTACTTCGAGC GGAGGCATCCGGAGCTTGCAGGATCGCCGCGGCTCCGGGCGTAT ATGCTCCGCATTGGTCTTGACCAACTCTATCAGAGCTTGGTTGAC GGCAATTTCGATGATGCAGCTTGGGCGCAGGGTCGATGCGACGC AATCGTCCGATCCGGAGCCGGGACTGTCGGGCGTACACAAATCG CCCGCAGAAGCGCGGCCGTCTGGACCGATGGCTGTGTAGAAGTA CTCGCCGATAGTGGAAACCGACGCCCCAGCACTCGTCCGAGGGC AAAGGAATAG 104 PpPEP4 ATTTGAGTCACCTGCTTTAGGGCTGGAAGATATTTGGTTACTAGA region TTTTAGTACAAACTCTTGCTTTGTCAATGACATTAAAATAGGCAA (including GAATCGCAAAACTCAAATATTTCATGGAGATGAGATATGCTTGTT upstream CAAAGATGCCCAGAAAAAAGAGCAACTCGTTTATAGGGTTCATA knock-out TTGATGATGGAACAGGCCTTTTCCAGGGAGGTGAAAGAACCCAA fragment, GCCAATTCTGATGACATTCTGGATATTGATGAGGTTGATGAAAA promoter, GTTAAGAGAACTATTGACAAGAGCCTCAAGGAAACGGCATATCA open CCCCTGCATTGGAAACTCCTGATAAACGTGTAAAAAGAGCTTATT reading TGAACAGTATTACTGATAACTCTTGATGGACCTTAAAGATGTATA frame, and ATAGTAGACAGAATTCATAATGGTGAGATTAGGTAATCGTCCGG downstream AATAGGAATAGTGGTTTGGGGCGATTAATCGCACCTGCCTTATAT knock- GGTAAGTACCTTGACCGATAAGGTGGCAACTATTTAGAACAAAG out CAAGCCACCTTTCTTTATCTGTAACTCTGTCGAAGCAAGCATCTT fragment) TACTAGAGAACATCTAAACCATTTTACATTCTAGAGTTCCATTTC TCAATTACTGATAATCAATTTAAAGATGATATTTGACGGTACTAC GATGTCAATTGCCATTGGTTTGCTCTCTACTCTAGGTATTGGTGCT GAAGCCAAAGTTCATTCTGCTAAGATACACAAGCATCCAGTCTC AGAAACTTTAAAAGAGGCCAATTTTGGGCAGTATGTCTCTGCTCT GGAACATAAATATGTTTCTCTGTTCAACGAACAAAATGCTTTGTC CAAGTCGAATTTTATGTCTCAGCAAGATGGTTTTGCCGTTGAAGC TTCGCATGATGCTCCACTTACAAACTATCTTAACGCTCAGTATTT TACTGAGGTATCATTAGGTACCCCTCCACAATCGTTCAAGGTGAT TCTTGACACAGGATCCTCCAATTTATGGGTTCCTAGCAAAGATTG TGGATCATTAGCTTGCTTCTTGCATGCTAAGTATGACCATGATGA GTCTTCTACTTATAAGAAGAATGGTAGTAGCTTTGAAATTAGGTA TGGATCCGGTTCCATGGAAGGGTATGTTTCTCAGGATGTGTTGCA AATTGGGGATTTGACCATTCCCAAAGTTGATTTTGCTGAGGCCAC ATCGGAGCCGGGGTTGGCCTTCGCTTTTGGCAAATTTGACGGAAT TTTGGGGCTTGCTTATGATTCAATATCAGTAAATAAGATTGTTCC TCCAATTTACAAGGCTTTGGAATTAGATCTCCTTGACGAACCAAA ATTTGCCTTCTACTTGGGGGATACGGACAAAGATGAATCCGATG GCGGTTTGGCCACATTTGGTGGTGTGGACAAATCTAAGTATGAA GGAAAGATCACCTGGTTGCCTGTCAGAAGAAAGGCTTACTGGGA GGTCTCTTTTGATGGTGTAGGTTTGGGATCCGAATATGCTGAATT GCAAAAAACTGGTGCAGCCATCGACACTGGAACCTCATTGATTG CTTTGCCCAGTGGCCTAGCTGAAATTCTCAATGCAGAAATTGGTG CTACCAAGGGTTGGTCTGGTCAATACGCTGTGGACTGTGACACTA GAGACTCTTTGCCAGACTTAACTTTAACCTTCGCCGGTTACAACT TTACCATTACTCCATATGACTATACTTTGGAGGTTTCTGGGTCAT GTATTAGTGCTTTCACCCCCATGGACTTTCCTGAACCAATAGGTC CTTTGGCAATCATTGGTGACTCGTTCTTGAGAAAATATTACTCAG TTTATGACCTAGGCAAAGATGCAGTAGGTTTAGCCAAGTCTATTT AGGCAAGAATAAAAGTTGCTCAGCTGAACTTATTTGGTTACTTAT CAGGTAGTGAAGATGTAGAGAATATATGTTTAGGTATTTTTTTTT AGTTTTTCTCCTATAACTCATCTTCAGTACGTGATTGCTTGTCAGC TACCTTGACAGGGGCGCATAAGTGATATCGTGTACTGCTCAATCA AGATTTGCCTGCTCCATTGATAAGGGTATAAGAGACCCACCTGCT CCTCTTTAAAATTCTCTCTTAACTGTTGTGAAAATCATCTTCGAA GCAAATTCGAGTTTAAATCTATGCGGTTGGTAACTAAAGGTATGT CATGGTGGTATATAGTTTTTCATTTTACCTTTTACTAATCAGTTTT ACAGAAGAGGAACGTCTTTCTCAAGATCGAAATAGGACTAAATA CTGGAGACGATGGGGTCCTTATTTGGGTGAAAGGCAGTGGGCTA CAGTAAGGGAAGACTATTCCGATGATGGAGATGCTTGGTCTGCT TTTCCTTTTGAGCAATCTCATTTGAGAACTTATCGCTGGGGAGAG GATGGACTAGCTGGAGTCTCAGACAATCATCAACTAATTTGTTTC TCAATGGCACTGTGGAATGAGAATGATGATATTTTGAAGGAGCG ATTATTTGGGGTCACTGGAGAGGCTGCAAATCATGGAGAGGATG TTAAGGAGCTTTATTATTATCTTGATAATACACCTTCTCACTCTTA TATGAAATACCTTTACAAATATCCACAATCGAAATTTCCTTACGA AGAATTGATTTCAGAGAACCGTAAACGTTCCAGATTAGAAAGAG AGTACGAGATTACTGACTCTGAAGTACTGAAGGATAACAGATAT TTTGATGTGATCTTTGAAATGGCAAAGGACGATGAAGATGAGAA TGAACTTTACTTTAGAATTACCGCTTACAACCGAGGTCCCACCCC TGCCCCTTTACATGTCGCTCCACAGGTAACCTTTAGAAATACCTG GTCCTGGGGTATAGATGAGGAAAAGGATCACGACAAACCTATAG CTTGCAAGGAATACCAAGACAACAACTATTCTATTCGGTTAGAT AGTT 105 Ashbya GATCTGTTTAGCTTGCCTCGTCCCCGCCGGGTCACCCGGCCAGCG gossypii ACATGGAGGCCCAGAATACCCTCCTTGACAGTCTTGACGTGCGC TEF1 AGCTCAGGGGCATGATGTGACTGTCGCCCGTACATTTAGCCCATA promoter CATCCCCATGTATAATCATTTGCATCCATACATTTTGATGGCCGC ACGGCGCGAAGCAAAAATTACGGCTCCTCGCTGCAGACCTGCGA GCAGGGAAACGCTCCCCTCACAGACGCGTTGAATTGTCCCCACG CCGCGCCCCTGTAGAGAAATATAAAAGGTTAGGATTTGCCACTG AGGTTCTTCTTTCATATACTTCCTTTTAAAATCTTGCTAGGATACA GTTCTCACATCACATCCGAACATAAACAACC 106 Ashbya TAATCAGTACTGACAATAAAAAGATTCTTGTTTTCAAGAACTTGT gossypii CATTTGTATAGTTTTTTTATATTGTAGTTGTTCTATTTTAATCAAA TEF1 TGTTAGCGTGATTTATATTTTTTTTCGCCTCGACATCATCTGCCCA termination GATGCGAAGTTAAGTGCGCAGAAAGTAATATCATGCGTCAATCG sequence TATGTGAATGCTGGTCGCTATACTGCTGTCGATTCGATACTAACG CCGCCATCCAGTGTCGAAAAC

While the present invention is described herein with reference to illustrated embodiments, it should be understood that the invention is not limited hereto. Those having ordinary skill in the art and access to the teachings herein will recognize additional modifications and embodiments within the scope thereof. Therefore, the present invention is limited only by the claims attached herein. 

1. A method for producing a recombinant glycoprotein in Pichia pastoris that lacks detectable cross binding activity with antibodies made against host cell antigens, comprising: (a) providing a recombinant Pichia pastoris host cell which does not display β-mannosyltransferase 2 activity with respect to an N-glycan or O-glycan and does not display at least one activity selected from β-mannosyltransferase 1 activity and β-mannosyltransferase 3 activity with respect to an N-glycan or O-glycan and which includes a nucleic acid molecule encoding the recombinant glycoprotein; (b) growing the host cell in a medium under conditions effective for expressing the recombinant glycoprotein; and (c) recovering the recombinant glycoprotein from the medium to produce the recombinant glycoprotein that lacks detectable cross binding activity with antibodies made against host cell antigens.
 2. The method of claim 1, wherein the host cell does not display β-mannosyltransferase 2 activity, β-mannosyltransferase 1 activity, and β-mannosyltransferase 3 activity with respect to an N-glycan or O-glycan.
 3. The method of claim 1, wherein the host cell further does not display β-mannosyltransferase 4 activity with respect to an N-glycan or O-glycan.
 4. The method of claim 1, wherein the detectable cross binding activity with antibodies made against host cell antigens is determined in a sandwich ELISA.
 5. The method of claim 1, wherein the detectable cross binding activity with antibodies made against host cell antigens is determined in a Western blot.
 6. The method of claim 1, wherein: (i) the recombinant glycoprotein is a therapeutic glycoprotein (ii) the therapeutic glycoprotein is selected from the group consisting erythropoietin (EPO); cytokines such as interferon α, interferon β, interferon γ, and interferon ω; and granulocyte-colony stimulating factor (GCSF); GM-CSF; coagulation factors such as factor VIII, factor IX, and human protein C; antithrombin III; thrombin; soluble IgE receptor α-chain; immunoglobulins such as IgG, IgG fragments, IgG fusions, and IgM; immunoadhesions and other Fc fusion proteins such as soluble TNF receptor-Fc fusion proteins; RAGE-Fc fusion proteins; interleukins; urokinase; chymase; and urea trypsin inhibitor; IGF-binding protein; epidermal growth factor; growth hormone-releasing factor; annexin V fusion protein; angiostatin; vascular endothelial growth factor-2; myeloid progenitor inhibitory factor-1; osteoprotegerin; α-1-antitrypsin; α-feto proteins; DNase II; kringle 3 of human plasminogen; glucocerebrosidase; TNF binding protein 1; follicle stimulating hormone; cytotoxic T lymphocyte associated antigen 4—Ig; transmembrane activator and calcium modulator and cyclophilin ligand; glucagon like protein 1; and IL-2 receptor agonist; (iii) the host cell is genetically engineered to produce glycoproteins that have human-like N-glycans; and/or (iv) the host cell is genetically engineered to produce glycoproteins that have predominantly an N-glycan selected from Man₅GlcNAc₂, Man₃GlcNAc₂, GlcNAcMan₅GlcNAc₂, GalGlcNAcMan₅GlcNAc₂, NANAGalGlcNAcMan₅GlcNAc₂, GlcNAcMan₃GlcNAc₂, GlcNAc₍₁₋₄₎Man₃GlcNAc₂, Gal₍₁₋₄₎GlcNAc₍₁₋₄₎Man₃GlcNAc₂, and NANA₍₁₋₄₎Gal₍₁₋₄₎GlcNAc₍₁₋₄₎Man3GlcNAc2.
 7. (canceled)
 8. (canceled)
 9. (canceled)
 10. A composition comprising one or more recombinant glycoproteins obtained by the method of claim
 1. 11. A method for producing a mature human erythropoietin in Pichia pastoris comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens, comprising: (a) providing a recombinant Pichia pastoris host cell genetically engineered to produce sialic acid-terminated biantennary N-glycans and does not display a β-mannosyltransferase 2 activity with respect to an N-glycan or O-glycan, and does not display at least one activity selected from a β-mannosyltransferase 1 activity and a β-mannosyltransferase 3 activity with respect to an N-glycan or O-glycan and which includes two or more nucleic acid molecules, each encoding a fusion protein comprising a mature human erythropoietin fused to a signal peptide that targets the ER and which is removed when the fusion protein is in the ER; (b) growing the host cell in a medium under conditions effective for expressing and processing the first and second fusion proteins; and (c) recovering the mature human erythropoietin from the medium to produce the mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens.
 12. The method of claim 11, wherein the host cell does not display β-mannosyltransferase 2 activity, β-mannosyltransferase 1 activity, and β-mannosyltransferase 3 activity with respect to an N-glycan or O-glycan.
 13. The method of claim 12, wherein the host cell further does not display β-mannosyltransferase 4 activity with respect to an N-glycan or O-glycan.
 14. The method of claim 11, wherein the signal peptide is a S. cerevisiae αMATpre signal peptide or a chicken lysozyme signal peptide.
 15. The method of claim 11, wherein at least one nucleic acid molecule encodes a fusion protein wherein the erythropoietin is fused to the S. cerevisiae αMATpre signal peptide and at least one nucleic acid molecule encodes a fusion protein wherein the erythropoietin is fused to the S. cerevisiae αMATpre signal peptide a chicken lysozyme signal peptide.
 16. The method of claim 11, wherein the codons of the nucleic acid sequence of the nucleic acid molecule encoding the erythropoietin is optimized for expression in Pichia pastoris.
 17. The method of claim 11, wherein the detectable cross binding activity with antibodies made against host cell antigens is determined in a sandwich ELISA.
 18. The method of claim 11, wherein the detectable cross binding activity with antibodies made against host cell antigens is determined in a Western blot.
 19. The method of claim 11, wherein recovering the mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens from the medium includes a cation exchange chromatography step.
 20. The method of claim 11, wherein recovering the mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens from the medium includes a hydroxyapatite chromatography step.
 21. The method of claim 11, wherein recovering the mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens from the medium includes an anion exchange chromatography step.
 22. A composition comprising a mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens obtained from the method of claim 18 and a pharmaceutically acceptable salt.
 23. The composition of claim 22, wherein the mature human erythropoietin comprising predominantly sialic acid-terminated biantennary N-glycans and having no detectable cross binding activity with antibodies made against host cell antigens is conjugated to a hydrophilic polymer. 